I think I’m not getting what the -q option in pileup is doing. From the man page, it says:
-q, -min-MQ INT Minimum mapping quality for an alignment to be used [0] I had assumed that for higher values of q, I would get, if anything, fewer variant sites and fewer called variants at those sites. However, when I used several values for -q, I found that the larger the value of q, the larger the size of the resulting vcf file for a ~3MB region in about ~300 people, the file for -q 5 was ~190K lines, but the file for -q 40 was ~197k lines. The options used are: samtools mpileup -A -uv -q <number> -v -t DP,DPR,DV,DP4,INFO/DPR,SP -l <site_list> -f <fa file> -I <list of ~300 individual bam files> | bcftools call -vmO v -f GQ > qsamtools.vcf Better understanding of the -q option and suggestions would be much appreciated. Thanks, Warwick Daw ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
