Rui:Haplotyping 6.21.11

From ZhangLabWiki
Jump to navigation Jump to search

Haplotyping 6.21.11[edit]

Data[edit]

ruiliu@genome-miner:~$ cd /home/kunzhang/haplotyping/Data/HL095/

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ ls -l s_4_Indx1.*

-rw-r--r-- 1 kunzhang kunzhang 114237942 2011-06-13 22:07 s_4_Indx1.bowtie.pileup
-rw-r--r-- 1 kunzhang kunzhang  39977658 2011-06-13 21:28 s_4_Indx1.bowtie.sorted.bam
-rw-r--r-- 1 kunzhang kunzhang   4442210 2011-06-13 22:05 s_4_Indx1.bowtie.sorted.unique.bam
-rw-r--r-- 1 kunzhang kunzhang       278 2011-06-13 21:29 s_4_Indx1.bowtie.variants.txt
-rw-r--r-- 1 kunzhang kunzhang      7103 2011-06-14 15:58 s_4_Indx1.hapCompare.txt
-rw-r--r-- 1 kunzhang kunzhang      9399 2011-06-14 16:56 s_4_Indx1.idioGraph.txt
-rw-r--r-- 1 kunzhang kunzhang    675115 2011-06-13 21:29 s_4_Indx1.log
-rw-r--r-- 1 kunzhang kunzhang 273522562 2011-06-13 18:08 s_4_Indx1.txt

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ less s_4_Indx1.bowtie.pileup

1       557399  C       A       25      25      25      1       ^:A     f
1       557400  A       A       25      0       25      1       .       f
1       557401  T       T       25      0       25      1       .       f
1       557402  C       C       25      0       25      1       .       f
1       557403  A       A       25      0       25      1       .       c
1       557404  C       C       25      0       25      1       .       g
1       557405  T       T       25      0       25      1       .       g
1       557406  A       A       25      0       25      1       .       g
1       557407  G       G       25      0       25      1       .       g
1       557408  A       A       25      0       25      1       .       e
1       557409  C       C       25      0       25      1       .       f

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ more s_4_Indx11.log

/home/kunzhang/softwares/bowtie-latest/bowtie -k 1 -l 32 -n 2 -m 1 --best --quiet -p 4 /home/kunzhang/HsGenome/1KG.ref/HsB36m s_4_Indx
11.txt s_4_Indx11.bowtie.map.1 
/home/kunzhang/Exome/Data/scripts/trimTerminalMismatches.pl < s_4_Indx11.bowtie.map.1 > s_4_Indx11.bowtie.map.2
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/bowtie2sam.pl  s_4_Indx11.bowtie.map.2 > s_4_Indx11.bowtie.sam
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools import /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa.gz.fai s_4_Indx
11.bowtie.sam s_4_Indx11.bowtie.bam
[sam_header_read2] 114 sequences loaded.
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools sort s_4_Indx11.bowtie.bam  s_4_Indx11.bowtie.sorted
java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.38/MarkDuplicates.jar ASSUME_SORTED=TRUE REMOVE_DUPLICATES=TRUE INPUT=s_4_In
dx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.unique.bam METRICS_FILE=dup.metric
[Tue Jun 14 15:23:03 PDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=s_4_Indx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.uni
que.bam METRICS_FILE=dup.metric REMOVE_DUPLICATES=true ASSUME_SORTED=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDL
ES_FOR_READ_ENDS_MAP=8000 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 TMP_DIR
=/tmp/kunzhang VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=fals
e CREATE_MD5_FILE=false
INFO	2011-06-14 15:23:03	MarkDuplicates	Start of doWork freeMemory: 374846832; totalMemory: 377225216; maxMemory: 1908932608
INFO	2011-06-14 15:23:03	MarkDuplicates	Reading input file and constructing read end information.
INFO	2011-06-14 15:23:03	MarkDuplicates	Will retain up to 7575129 data points before spilling to disk.
INFO	2011-06-14 15:23:03	MarkDuplicates	Assuming input is coordinate sorted.
INFO	2011-06-14 15:23:06	MarkDuplicates	Read 887559 records. 0 pairs never matched.
INFO	2011-06-14 15:23:07	MarkDuplicates	After buildSortedReadEndLists freeMemory: 733397640; totalMemory: 925368320; maxMemory
: 1908932608
INFO	2011-06-14 15:23:07	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
INFO	2011-06-14 15:23:07	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2011-06-14 15:23:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2011-06-14 15:23:09	MarkDuplicates	Sorting list of duplicate records.
INFO	2011-06-14 15:23:09	MarkDuplicates	After generateDuplicateIndexes freeMemory: 923987040; totalMemory: 1410072576; maxMemo
ry: 1908932608
INFO	2011-06-14 15:23:09	MarkDuplicates	Marking 837865 records as duplicates.
INFO	2011-06-14 15:23:09	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2011-06-14 15:23:12	MarkDuplicates	Before output close freeMemory: 920285040; totalMemory: 1408237568; maxMemory: 1908932
608
INFO	2011-06-14 15:23:12	MarkDuplicates	After output close freeMemory: 876964080; totalMemory: 1364918272; maxMemory: 19089326
08
[Tue Jun 14 15:23:12 PDT 2011] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=1364918272
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa s_4_Indx1
1.bowtie.sorted.unique.bam > s_4_Indx11.bowtie.pileup
Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145.
Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145.

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.bam | wc -l

887559

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.unique.bam | wc -l

49694

Reads[edit]

Barcode Reads Unique Percentage
Indx1 163556 15899 9.7
Indx2 196625 16718 8.5
Indx3 127140 10123 8.0
Indx4 189464 13511 7.1
Indx5 9536 4856 50.9
Indx6 220670 12779 5.8
Indx7 185404 12479 6.7
Indx8 209445 14185 6.8
Indx9 175999 12100 6.9
Indx10 212683 13919 6.5
Indx11 188707 14591 7.7
Indx12 326082 16300 5.0