Changes between Version 1 and Version 2 of SOPs/callingSNPs


Ignore:
Timestamp:
04/08/13 16:09:26 (12 years ago)
Author:
thiruvil
Comment:

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  • SOPs/callingSNPs

    v1 v2  
    77  #Use Q to set base quality threshold
    88  samtools mpileup -Q 25 -ugf <reference.fasta> <file.bam> | bcftools view -bvcg - > accepted_hits.raw.bcf
     9  #mpileup BAQ computation might be too stringent, disabling BAQ may be needed
     10  samtools mpileup -B -Q 25 -ugf <reference.fasta> <file.bam> | bcftools view -bvcg - > accepted_hits.raw.bcf
    911}}}
    1012