Hi, I am upgrading samtools/bcftools from 1.3.1 to 1.5 and I am trying to understand a difference I spotted.
Using bcftools 1.3.1: > samtools mpileup -uf ref.fna sample.bam | ./bcftools-1.3.1/bcftools call -c > --ploidy 1 - gyrA 284 . A G 77.0075 . DP=77;VDB=1.03743e-17;SGB=-0.693145;RPB=0.818901;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.5;AC1=1;DP4=7,30,32,8;MQ=20;FQ=79.9725;PV4=7.52472e-08,1,1,0.169748 GT:PL 0:107,127 Using bcftools 1.5: > samtools mpileup -uf ref.fna sample.bam | bcftools call -c --ploidy 1 - gyrA 284 . A . 49.9963 . DP=77;VDB=1.03743e-17;SGB=-0.693145;RPB=0.818901;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.5;AC1=0;DP4=7,30,32,8;MQ=20;FQ=-999;PV4=7.52472e-08,1,1,0.169748 GT:PL 0:107 in both cases samtools was version 1.5 I just wondered what has changed in bcftools for it to call the variant in version 1.3.1 but not in 1.5 ? By the way, the change must have happened between 1.3.1 and 1.4 as 1.4 gives the same result as 1.5 above) Looking at the release notes for 1.4, is this related to "Improved calculation of the QUAL score particularly for REF sites"? Thanks for any help Adam ------------------------------------------------------------------------------ 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