Dear list members, unfortunately I got no answer for a similar question I posted before. There seems to be a major bug regarding the coverage (DP4) calculation for indels.
The raw mpileup output shows one read with a 59bp deletion: 17 41243449 T 487 .$,$,$,,,,,a,,,,..............................G............................,.,...,.,.....,...................$.........,..,,,........,,,,,,,,,,,.,-59acctaagtttgaatccatgctttgctcttcttgattattttcttccaagcccgttcctc.,,,.....,..........................,,.......................,,.,,,.......,.........,,,,,,....,,,,,,,,,,,,,,,,,,,,,..........................,,,,,,,...,,.............,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,..,,,,.,.........,,.,,,,,,,,,..........................................................,,,,,,,,,,,.....................................,,,,,,.. -@.@@@?A-?@@BGGG<kD<<lGGlhGkfFGGDG,Gk=GFklG5GGGGGGlkkGGGGkFlGGGllGGGGkFk@FFlDGFk!lGG-GFGGGGGkjGGklDGGGlGVkGGGlGGcGjFGk!FFGklGGGXf!!F0E!EF!F!G!G!!!GGGDD!kGGkFGGGGGGlGGGFGDDklGGGGGF!KFlkGF+FHGlGGGkGGGlGkGk!!G!E!GhGGGGk!jFGlFFGGG!F!E!!GlG]!!FF!E!F!!!E!FFEF!!!!fHGklHGmkmGmGHBmlGHmGHGlGm!!!!!!!Gkb!!HmkGGHGGGGGGh!kk!!!EF!!E!E!1!FF!!!!!F!!E!!!EE!!H!l+!!!!G!GGlGGGhGk!!GF!!!!!!FEEEEEEiEiEE=EEEEEEjEE=EEEjjjEEEEEEEEEEEjiEEjEjEEEEEEEEEjEEE!!!!!!!!!!!EEjEEEEjEEEjEEEEEEEjEEEEjEEEEEEEjEEEE!!!!!!?A But in the vcf output of mpileup the first four I16 as well as the DP4 values make absolutely no sense to me, as they state there are 128 reads with this deletion (the alt allele coverage). Interestingly the IDV value is correct. 17 41243449 . TACCTAAGTTTGAATCCATGCTTTGCTCTTCTTGATTATTTTCTTCCAAGCCCGTTCCTC T 0 . INDEL;IDV=1;IMF=0.00205339;DP=487;I16=241,118,99,29,68020,1.56646e+07,2713,217509,21540,1.2924e+06,7680,460800,7645,179733,1048,10078;QS=0.90901,0.0909901;VDB=0.98454;SGB=-0.693147;MQSB=1;MQ0F=0;DPR=359,128 PL:DP:DV:DP4:DPR 166,0,255:487:128:241,118,99,29:359,128 Kind regards, Christian ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
