Truncating non-annotated variants #12
Description
I am using CAVA 1.2.3
I see truncation in the ouput.
I am requesting all variants be output.
I see some missing variants at the end of files.
and
If the input file is too small (and these variants are not in genes).
then cava says it processes "2" records, but outputs none.
Here is an example line that will produce no output.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_3595-ST-0002
1 17013774 . AAAAT A 674.73 . BaseQRankSum=0.850;ClippingRankSum=0.343;DP=52;MLEAC=1,0;MLEAF=0.500,0.00;MQ=60.00;MQRankSum=-0.127;ReadPosRankSum=0.741 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:712,0,667:7,8,8,10
1 17014589 . A G 418.77 . BaseQRankSum=0.580;ClippingRankSum=1.221;DP=31;MLEAC=1,0;MLEAF=0.500,0.00;MQ=60.00;MQRankSum=1.902;ReadPosRankSum=-0.020 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:447,0,263:5,8,8,10