I would suggest you use GATK rather then samtools
> On 20 Jun 2017, at 9:51 pm, Jody Phelan <jodyphe...@gmail.com> wrote: > > Hi all, > > I am trying to detect rare variants on a haploid organism using samtools > mpileup + bcftools call (htslib v1.4). > I have a few variants which I am expecting to see however they are not called > as variant. > > When I use the command like this: > > samtools mpileup -ugf ref.fa 1.bam | bcftools call --ploidy 1 -Am > > I get an output like this: > Chromosome 1473246 . A G 24.8295 . > DP=80;VDB=0.44194;SGB=-0.693021;RPB=0.139427;MQB=1;MQSB=1;BQB=0.993938;MQ0F=0;AC=0;AN=1;DP4=28,23,12,15;MQ=60 > GT:PL 0:255,255 > > From "DP4" I can see that there is quite a good 0.65:0.35 ratio for ref and > alt alleles. > > Now when I remove the -A flag and add the -v flag form bcftools call like so: > samtools mpileup -ugf ref.fa 1.bam | bcftools call --ploidy 1 -vm > > I do not get this variant. So my question: Is samtools not able to call mixed > variants? > I thought the -m flag in bcftools was used for this purpose? > If I use --ploidy ==1 does it always pick the major allele? > > Any help would be appreciated, > Thanks, > Jody > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
