Changes between Version 25 and Version 26 of SOPs/variant_calling


Ignore:
Timestamp:
10/18/18 11:51:49 (6 years ago)
Author:
gbell
Comment:

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  • SOPs/variant_calling

    v25 v26  
    6363In our experience, "-B" (disable BAQ) or "-E" (recalculate BAQ) works better than the default method, which can remove some obvious variants.
    6464{{{
    65 samtools mpileup -d100000 -t DP,AD,ADF,ADR,INFO/AD,SP -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa A_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| A_reads.bt2.sorted_unique.raw.bcf
     65samtools mpileup -d100000 -t DP,AD,ADF,ADR,SP,DP4,INFO/AD -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa A_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| A_reads.bt2.sorted_unique.raw.bcf
    6666#in bcftools call: -m for multi-allelic, -c for bi-alleleic
    6767}}}