Changes between Version 26 and Version 27 of SOPs/variant_calling


Ignore:
Timestamp:
10/18/18 11:57:21 (6 years ago)
Author:
gbell
Comment:

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  • SOPs/variant_calling

    v26 v27  
    6868Call variants (multiple sample vs. reference) using a set of BAM files
    6969{{{
    70 samtools mpileup -d100000 -t DP,AD,ADF,ADR,INFO/AD,SP -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa *_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| ALL_reads.bt2.sorted_unique.raw.bcf
     70samtools mpileup -d100000 -t DP,AD,ADF,ADR,SP,DP4,INFO/AD -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa *_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| ALL_reads.bt2.sorted_unique.raw.bcf
    7171}}}
    7272