EricChu:LabNotesMDA/2015-4-24

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Pair-End BWA on PGP1#21CoRE and GM20431-2Cell(Mar19)[edit]

  • Chris helped me to make a batch file to run BWA sampe. The inputs are the two filenames per chamber in a single line in txt file (eg.EC-PGP1num21CoRE.txt). The outputs are sorted BAM and unique BAM files.
  • In /media/Syn_15T/Eric_15T/150422RapidRunPairEnd,
vi create EC-PGP1num21CoRE.txt file,
perl batch_bwa_pe_fastq2bam.final.pl EC-PGP1num21CoRE.txt hg19 > EC-PGP1num21CoRE.log
vi create EC-GM20431-2C-Mar19.txt file,
perl batch_bwa_pe_fastq2bam.final.pl EC-GM20431-2C-Mar19.txt hg19 > EC-GM20431-2C-Mar19.log
  • Get coverage statistics
get_covstats.pl > EC_pairend_covstat.txt &
/home/kunzhang/softwares/samtools-latest/samtools flagstat EC-GM20431-2C-Mar19-VI-30_S14_L001_R1_001.sorted.bam > EC-GM20431-2C-Mar19-VI-30_S14_L001_R1_001.sorted.bam.stat
cat *.stat > flagstatall.log
/home/kunzhang/softwares/samtools-latest/samtools flagstat EC-PGP1num21CoRE-Feb25-29_S37_L002_R1_001.sorted.unique.bam > EC-PGP1num21CoRE-Feb25-29_S37_L002_R1_001.sorted.unique.bam.stat2
cat *.stat2 > flagstatunique.log
  • Pileup Chr4 with combined VCFs of BAC and HiC
/home/kunzhang/softwares/samtools-0.1.8/samtools pileup -Ac -f /GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -l /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/vcfs/sorted.chr4.pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final-het-final.modifiedINFO3_clean_final.vcf EC-GM20431-2C-Mar19-III-17_S1_L001_R1_001.sorted.bam > EC-GM17_sorted_multialign_SNP.txt