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i am using ASEReadCounter in order to count the number of reads per variant in a BAM file, and somehow related to a previous post (below), I am encountering a similar error :
"MESSAGE: More then one variant context at position: chr19:125517"
i.e. in the vcf file, there are 2 entries for the same position :
chr19 125517 . A G 42.01 . AC1=1;AF1=0.5;BQB=0.950129;DP=43;DP4=12,7,4,1;FQ=45.0154;MQ=46;MQ0F=0;MQB=0.984335;MQSB=0.998127;PV4=0.631094,1,1,1;RPB=1;SGB=-0.590765;VDB=0.233642 GT:PL 0/1:72,0,255
chr19 125517 . AA AAGAGA 5.79 . AC1=1;AF1=0.499984;DP=43;DP4=7,5,5,0;FQ=8.19012;IDV=2;IMF=0.0444444;INDEL;MQ=45;MQ0F=0;MQSB=0.99446;PV4=0.244505,1,0.0559047,0.273348;SGB=-0.590765;VDB=0.125771 GT:PL 0/1:42,0,151
The question would be : is there any way in GATK to remove these sites ? Of course, i could do it with a simple script outside GATK, although doing it outside GATK may complicate a bit the pipeline. Thank you very much !
ps : the previous post was :