EricChu:LabNotesMDA/2016-4-20

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Solving Pileup Dropout Alleles that Appeared in Freebayes VCF[edit]

  • When I examined the SNV called by Freebayes, I searched the VCF and the pileup of another chamber. If this position was covered in another chamber, it would either be identical SNV call or a REF call. Then I output the contradictions as 1. SNV call in Freebayes 2. Pileup call in same chamber 3. Pileup call in another chamber. I wanted to see the actual raw base at this position.
  • However I found sometimes only two lines output per contradiction. And I believed this position was identified as low quality by pileup.
  • First the output in comparing SNV in two chambers. Here I had SNV in chamber21 and all positions in chamber 23. Five contradictory positions were found. I would expect result like 118010892, 118012539 and 118049213, where it had 3 line output which showed the raw base and consensus. However, in 117992788 and 117995112, pileup was missing in the same chamber (chamber21).
more comparefreebayesPGP1_21_ch21toch23.contradiction.txt
chrX    117992788       .       C       T       184.729 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=8;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=56.25;MQMR=60;NS=1;NUMALT=1;ODDS=42.5355;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=291;QR=73;RO=2;RPL=5;RPP=4.09604;RPPR=3.0103;RPR=3;RUN=1;SAF=3;SAP=4.09604;SAR=5;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:RO:QR:AO:QA:GL   1:10:2:73:8:291:-19.55,0
chrX    117992788       c       C       255     0       59      122     .$,$,,.,,,,,,..,,,,,,.,,,.,.,,...........,......,..,,.,,,,,.,,.......,,,......,....,,,,,,,....,,...,,,,.,,........,..,..,..^],  BBB77FFFFFFF0IIIBIBFFIFBFFFBFFFIFFIFIFFIIIIIFFIIFIFFFFBIFIFFFFIFIFIIFFFFFIFFFFFIIF<IIFFIFFIFFFIFIIIFFIFFBIIFFFFFFFFFFBFFgB
chrX    117995112       .       G       A       57.6871 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=55.6667;MQMR=36;NS=1;NUMALT=1;ODDS=13.2829;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=107;QR=37;RO=1;RPL=0;RPP=9.52472;RPPR=5.18177;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1       GT:DP:RO:QR:AO:QA:GL    1:4:1:37:3:107:-6.62065,0
chrX    117995112       g       G       31      0       17      7       a,.,.+4GAAA.+4GAAA,     FII'FF<
chrX    118010892       .       C       A       2093.29 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=70;CIGAR=1X;DP=77;DPB=77;DPRA=0;EPP=9.09042;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=59.5857;MQMR=59;NS=1;NUMALT=1;ODDS=481.998;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2625;QR=252;RO=7;RPL=33;RPP=3.50664;RPPR=10.7656;RPR=37;RUN=1;SAF=27;SAP=10.9517;SAR=43;SRF=4;SRP=3.32051;SRR=3;TYPE=snp;technology.ILLUMINA=1      GT:DP:RO:QR:AO:QA:GL    1:77:7:252:70:2625:-211.449,0
chrX    118010892       c       C       178     0       59      50      ,....,,.,,,,,,,,,,,.,.,..,..,,,,,,,,,,.,,,..,,,..,      BBF<BFFFFIIIFIIIIIFIFIIIIIFI'IIfIIIIFfIIIFFIFFBFF_
chrX    118010892       c       A       43      247     59      80      ,aAAaaaAaa.AAaaaAAaaaaaaaaaA.,aaaaaAa,AaAAaaAa.aAaaaaAAaaaaaaaaAAAaaAAaaAAaA.AAA        BBBBBFFFFFBFBIIFIFI7F0IFIFFFIFFFIFBIFIIgFIIgIFEFIIIIfIFFFFIBFFBIIIFFFIFFFFFBBBBB
chrX    118012539       .       C       T       550.341 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=19;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=3.12459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=43.6842;MQMR=0;NS=1;NUMALT=1;ODDS=126.721;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=698;QR=0;RO=0;RPL=14;RPP=12.2676;RPPR=0;RPR=5;RUN=1;SAF=15;SAP=16.8392;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1      GT:DP:RO:QR:AO:QA:GL    1:19:0:0:19:698:-59.5734,0
chrX    118012539       c       C       69      0       44      14      .......,,.,,,.  FFFFFII'7F0<7I
chrX    118012539       c       T       70      117     41      33      tTTtTtTTTTTtTtTTt,Tttttt,TTtTttT,       BF<FBFFFIII'IBBI00I'0'00'FF0I'0F'
chrX    118049213       .       G       T       516.531 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=49;CIGAR=1X;DP=82;DPB=82;DPRA=0;EPP=12.9813;EPPR=16.3106;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=118.936;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1816;QR=1264;RO=32;RPL=17;RPP=12.9813;RPPR=16.3106;RPR=32;RUN=1;SAF=23;SAP=3.40914;SAR=26;SRF=18;SRP=4.09604;SRR=14;TYPE=snp;technology.ILLUMINA=1       GT:DP:RO:QR:AO:QA:GL    1:82:32:1264:49:1816:-51.1832,0
chrX    118049213       g       G       54      0       60      9       ,..,,,,,,       IIFFIFIIB
chrX    118049213       g       K       228     228     60      83      t$Tttttt,t,,ttTT,,ttTt,.TT.ct,$tt...,,.T.ttT..t..,,ttttTt.TT..tT,TTT,tTT.TTtt..T.TT,T   BFB<FFFFIIIFI<BI<FFFIIFBI<FIfIIFBIIFFFIIIIIIIFIIIIIIIFFIFIFIFFFFFBFFFBFFI'FFFFFFFdB
SNV not matching = 2634
Total matching SNV = 59
  • I could use tview to find that this position 117992788 was covered in chamber 21 but no result was found in quality pileup. I searched the position right before and after in the unfiltered pileup and they were found.
/home/kunzhang/softwares/samtools-0.1.19/samtools tview -p chrX:117992788 -d T /media/NAS2_volume1/Eric/Eric_LTS15T/PGP1_21_BWA_MEM/PGP1_21_ch21.sorted.fragment.bam
  117992791 117992801 117992811 117992821 117992831 117992841 117992851
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
YTAATGCAGCTGGTGACTTTAAATTGAAGCCAATATTCATTTATCATTCTGAAAATTCTAGGGTCCYTAAGAATTATGCC
TTAATGCAGCTGGTGACTTTA               TCATTTATCATTCTGAAAATTCTAGTGTCCTTAAGAATTATGCC
TTAATGCAGCTGGTGACTTTA               TCATTTATCATTCTGAAAATTCTAGGGTCCTTAAGAATTATGCC
ttaatgcagctggtgactttaaattg                                 agggtccttaagaattatgcc
TTAATGCAGCTGGTGACTTTAAATTGA                                          AGAATTATGCC
CTAATGCAGCTGGTGACTTTAAATTGAAGCCAATATTC
ttaatgcagctggtgactttaaattgaagccaatattcattt
ctaatgcagctggtgactttaaattgaagccaatattcatttatcattctgaaaattctagggtccttaag
ttaatgcagctggtgactttaaattgaagccaatattcatttatcattctgaaaattctagggtccttaagaatt
ttaatgcagctggtgactttaaattgaagccaatattcatttatcattctgaaaattctaggg
ttaatgcagctggtgactttaaattgaagccaatattcatttatcattctgaaaattctaggg
  AATGCAGCTGGTGACTTTAAATTGAAGCCAATATTCATTTATCATTCTGAAAATTCTAGGGTCCCTAAGAATTATGCC
           GGTGACTTTAAATTGAAGCCAATATTCATTTATCATTCTGAAAATTCTAGGGTCCTTAAGAATTATGCC

PGP1_21_ch21.hemichrX.clean.pileup:chrX 117992789       t       T       57      0       57      10      ..,..,,,,,      BFIFFBIBFF
PGP1_21_ch23.hemichrX.clean.pileup:chrX 117992789       t       T       255     0       59      120     ,$,$.,,,,,,..,,,,,,.,,,.,.,,...........,-1a......,..,,.,,,,,.,,.......,,,......,....,,,,,,,....,,...,,,,.,,........,..,..,..,    BB<FFFFFFF<IIFFIFF<IFBIFBFF0FFFIIFFFIIIIIIF<IIIFBIFFFIIIFIFFIIBIIFFIIIFIIIIIFIIF<FIFFIFFIFFIIFIIIIFIFFFIIFFFFFFFFBFFFFgF
$ grep 117992787 *.pileup
PGP1_21_ch21.hemichrX.clean.pileup:chrX 117992787       g       G       57      0       57      10      ..,..,,,,,      FFIFFIBFFB
PGP1_21_ch23.hemichrX.clean.pileup:chrX 117992787       g       G       255     0       59      121     .,,,.,,,,,,..,,,,,,.,,,.,.,,...........,......,..,,.,,,,,.,,.......,,,......,....,,,,,,,....,,...,,,,.,,........,..,..,..        FBBB0FFFFFIFBIIFFIBFFIFFIFBBFFFIBFIBFFFIIFIIFIIIFIFIFFFIIIFFFFFFIIIFFFIFFIIFFFFIF'B<IFFII<FFFIIBIIBFFIFFFFFFFFFFFFFFFFBBg
$ grep 117992788 *.pileup
PGP1_21_ch23.hemichrX.clean.pileup:chrX 117992788       c       C       255     0       59      122     .$,$,,.,,,,,,..,,,,,,.,,,.,.,,...........,......,..,,.,,,,,.,,.......,,,......,....,,,,,,,....,,...,,,,.,,........,..,..,..^],   BBB77FFFFFFF0IIIBIBFFIFBFFFBFFFIFFIFIFFIIIIIFFIIFIFFFFBIFIFFFFIFIFIIFFFFFIFFFFFIIF<IIFFIFFIFFFIFIIIFFIFFBIIFFFFFFFFFFBFFgB
  • Then I ran pileup again. And found this position was called with a final low quality score.
/home/kunzhang/softwares/samtools-0.1.19/samtools view -b /media/NAS2_volume1/Eric/Eric_LTS15T/PGP1_21_BWA_MEM/PGP1_21_ch21.sorted.fragment.bam chrX:117992000-118011000 > PGP1_21_ch21_chrXextract.bam
/home/kunzhang/softwares/samtools-0.1.8/samtools pileup -Ac -f /GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa PGP1_21_ch21_chrXextract.bam > PGP1_21_ch21_chrXextract.notBQ0.pileup
grep 117992788 PGP1_21_ch21_chrXextract.notBQ0.pileup
chrX    117992788       c       Y       16      67      57      10      TTtT.t,ttt      BFIFBFIFFB
grep 117995112 PGP1_21_ch21_chrXextract.notBQ0.pileup
chrX    117995112       g       A       6       41      24      20      aa,,.,....,.**,+4gaaa.+4GAAA.+4GAAAaaA  BFFF0FIFFIFI0F0FFFBF
chrX    117995112       *       +GAAA/+GAAA     98      139     24      20      +GAAA   *       3       17      0       0       0


             117995121 117995131 117995141     117995151 117995161 117995171
N****NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN****NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
R    GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA    AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATCTATCT
a****GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATCTATCT
a****gaa         GAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATCTATCT
g****gaaag       gaaagaaagaaagaaaga****aagaaagaaagaaagaaagaaagaaagaaagaaatctatct
g****gaaaga       aaagaaagaaagaaaga****aagaaagaaagaaagaaagaaag*aagaaagaaatctatct
G****GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAA gaaagaaagaaagaaagaaagaaagaaatctatct
g****gaaagaaagaaagaaagaaagaaagaaaga****aagaaagaaagaaagaa GAAAGAAAGAAAGAAATCTATCT
G****GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAA GAAAGAAAGAAATCTATCT
G****GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAA GAAATCTATCT
G****GAAAGAAAGAAGGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA  tctatct
G****GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAA  AAAGAAAGAAATCTATCT
g****gaaagaaagaaagaaagaaagaaagaaagaaaggaagaaagaaagaaagaaagaaagaaagaaagaaatctatct
G****GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA   CTATCT
*****gaaagaaagaaagaaagaaagaaagaaaga****aagaaagaaagaaagaaagaaagaaagaaagaaatctatct
*****gaaagaaagaaagaaagaaagaaagaaaga****aagaaagaaagaaagaaagaaagaaagaaagaaatctatct
ggaaagaaagaaagaaagaaagaaagaaagaaaga****aagaaagaaagaaagaaagaaagaaagaaagaaatctatct
GGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATCTATCT
GGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATCTATCT
a****gaaagaaagaaagaaagaaagaaagaaaga****aagaaagaaagaaagaaagaaagaaagaaagaaatctatct
a****gaaagaaagaaagaaagaaagaaagaaaga****aagaaagaaagaaagaaagaaagaaagaaagaaatctatct
A****GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATCTATCT
     gaaagaaagaaagaaagaaagaaagaaaga****aagaaagaaagaaagaaagaaagaaagaaagaaatctatct
                     GAAAGAAAGAAAGA****AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATCTATCT
  • I checked all 5 of them with CGI and none of them were found as SNPs.
grep 118010892 pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf
grep 118012539 pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf
grep 118049213 pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf
grep 117992788 pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf
grep 117995112 pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final.vcf


  • Freebayes called an SNV in one chamber but not in another chamber, while pileup called the same SNV in two different chambers.
comparefreebayesPGP1_21_ch22toch23.contradiction.txt
::::::::::::::
chrX    117932997       .       G       T       44.144  .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=3;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=9.52472;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=32;NS=1;NUMALT=1;ODDS=10.1645;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=117;QR=66;RO=2;RPL=3;RPP=9.52472;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;technology.ILLUMINA=1    GT:DP:RO:QR:AO:QA:GL    1:5:2:66:3:117:-5.31748,0
chrX    117932997       g       T       78      93      16      23      Tt.TTTTtTTttttTTtTTtTtT <F0<<FBF<B'FBBF<BFIBBBF
chrX    117932997       g       T       92      153     18      72      ,$,$.,,,.tT.tTTTTtTttTtTTTTttTttTtTttttttttTTtttTttttttTTTTTTt,tTTTTttttTt     BB0F<F'FB'I<B<<F<IIBF'<00FF<B<BBB<FB7BFBBBBFBB<BB<BBFBFFIFFB'BFFB<0'70FB
chrX    117961469       .       C       T       2217.29 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=76;CIGAR=1X;DP=84;DPB=84;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=510.55;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2741;QR=247;RO=7;RPL=35;RPP=4.03889;RPPR=3.32051;RPR=41;RUN=1;SAF=33;SAP=5.8675;SAR=43;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;technology.ILLUMINA=1      GT:DP:RO:QR:AO:QA:GL    1:84:7:247:76:2741:-223.544,0
chrX    117961469       C       C       81      0       60      18      .$.$,.,,,,,..,...,,.    7<IFIFFFI<FF<BIBFI
chrX    117961469       C       T       46      204     60      89      T$T$tTtTtttTtttG.TTttttTTgTTTttTTTt,ttTttttt.,,TTTTtTTtTtTttt.ttTttt,tTTTTTTtttttTTTttttttT     70FFF7IIIFFII'F<<IIFIBBIFBFIF7FBFFFFFIIFIFFFBIBFIFFI<FFIBBFB<FFBBBBeFIBBIFIBBFFFF0F<00BFB
SNV not matching = 1014
Total matching SNV = 33

Summary of Freebayes SNV compare to All Overlap Positions in Hemizygous X[edit]

Total SNV found in PGP1#21 by Freebayes (ploidy1) = 17978 True Positive (CGI compare) = 15635 Total SNV found in PGP1#22 by Freebayes (ploidy1) = 8065 True Positive (CGI compare) = 7056

For PGP1#21, Identical Freebayes SNVs in two chambers (PGP1#21) = 750 (different than http://genome-tech.ucsd.edu/LabNotes/index.php/EricChu:LabNotesMDA/2016-4-15?) Freebayes SNV call mismatched Pileup call (REF or ALT) in another chamber = 69 (Basically mismatch call between two chambers) Worst mismatched SNV to another chamber (chamber 14 and 24) = 20 total Freebayes SNV call in 1st chamber mismatched Freebayes REF call (two Pileup calls were identical to 1st chamber) = 5 (False Negative from Freebayes) The two strand coverage was 1,388,149bp and one strand coverage was 23,131,132bp (total 24,519,281bp) @ DP=5, Q>3 True Positives (same as CGI)= False Positives (different than CGI)=


  • Compare Freebayes SNV to CGI SNP in chamber 5 PGP1#21 to find true positives. 6 were true and 2 were false positive. If set cutoff Qual at 165, all would be correct.
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  PGP1_21_05
chrX    151060570       .       T       G       23015.1 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=687;CIGAR=1X;DP=692;DPB=692;DPRA=0;EPP=8.32361;EPPR=9.52472;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5299.41;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=25835;QR=99;RO=3;RPL=360;RPP=6.45242;RPPR=9.52472;RPR=327;RUN=1;SAF=340;SAP=3.16518;SAR=347;SRF=0;SRP=9.52472;SRR=3;TYPE=snp;technology.ILLUMINA=1 GT:DP:RO:QR:AO:QA:GL    1:692:3:99:687:25835:-2304.24,0
chrX    151061540       .       C       T       54705.4 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=1622;CIGAR=1X;DP=1633;DPB=1633;DPRA=0;EPP=6.09481;EPPR=7.35324;GTI=0;LEN=1;MEANALT=2;MQM=59.9895;MQMR=60;NS=1;NUMALT=1;ODDS=12596.4;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61759;QR=307;RO=8;RPL=1005;RPP=204.553;RPPR=7.35324;RPR=617;RUN=1;SAF=926;SAP=73.8308;SAR=696;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;technology.ILLUMINA=1        GT:DP:RO:QR:AO:QA:GL    1:1633:8:307:1622:61759:-5500.91,0
chrX    151061597       .       T       G       44136.4 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=1331;CIGAR=1X;DP=1334;DPB=1334;DPRA=0;EPP=119.315;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQM=59.9812;MQMR=0;NS=1;NUMALT=1;ODDS=10162.8;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=49448;QR=0;RO=0;RPL=611;RPP=22.3937;RPPR=0;RPR=720;RUN=1;SAF=695;SAP=8.68941;SAR=636;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1     GT:DP:RO:QR:AO:QA:GL    1:1334:0:0:1331:49448:-4432.83,0
chrX    151062485       .       T       G       105.195 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=24.2221;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=136;QR=0;RO=0;RPL=4;RPP=11.6962;RPPR=0;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1       GT:DP:RO:QR:AO:QA:GL    1:4:0:0:4:136:-12.5756,0
chrX    151075915       .       G       A       1505.54 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=48;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.9056;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=58.4375;MQMR=0;NS=1;NUMALT=1;ODDS=346.663;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1728;QR=0;RO=0;RPL=29;RPP=7.5342;RPPR=0;RPR=19;RUN=1;SAF=33;SAP=17.6677;SAR=15;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1  GT:DP:RO:QR:AO:QA:GL    1:48:0:0:48:1728:-155.577,0
chrX    151133898       .       G       A       785.731 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=24;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=180.921;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=904;QR=0;RO=0;RPL=10;RPP=4.45795;RPPR=0;RPR=14;RUN=1;SAF=14;SAP=4.45795;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1      GT:DP:RO:QR:AO:QA:GL    1:24:0:0:24:904:-81.3697,0
chrX    151138179       .       A       C       6315.43 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=190;CIGAR=1X;DP=190;DPB=190;DPRA=0;EPP=3.19316;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1454.18;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7088;QR=0;RO=0;RPL=94;RPP=3.05602;RPPR=0;RPR=96;RUN=1;SAF=105;SAP=7.58182;SAR=85;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:RO:QR:AO:QA:GL    1:190:0:0:190:7088:-635.736,0
chrX    151155667       .       T       C       161.304 .       AB=0;ABP=0;AC=1;AF=1;AN=1;AO=9;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=22.5536;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.1415;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=297;QR=37;RO=1;RPL=0;RPP=22.5536;RPPR=5.18177;RPR=9;RUN=1;SAF=9;SAP=22.5536;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1       GT:DP:RO:QR:AO:QA:GL    1:10:1:37:9:297:-23.3551,0
more PGP1_21_ch05.freebayes.chrX.CGIcommon.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  GS00253-DNA_D02_200_37-ASM
chrX    151060570       rs5970148       T       G       -1      PASS    COL8    GT:GQ:HQ        0/1:-1:-1,-1
chrX    151061540       rs5970150       C       T       -1      PASS    COL8    GT:GQ:HQ        0/1:-1:-1,-1
chrX    151061597       rs5925068       T       G       -1      PASS    COL8    GT:GQ:HQ        0/1:-1:-1,-1
chrX    151075915       rs6526050       G       A       -1      PASS    COL8    GT:GQ:HQ        0/1:-1:-1,-1
chrX    151133898       rs5925075       G       A       -1      PASS    COL8    GT:GQ:HQ        0/1:-1:-1,-1
chrX    151138179       rs1139916       A       C       -1      PASS    COL8    GT:GQ:HQ        0/1:-1:-1,-1
  • Getting true positive SNV in PGP1#22
more PGP1_22_ch*.CGIcommon.vcf > PGP1_22.truepositive.CGIcommon.vcf