Hello all,
Which are the possible values and meanings of the first column in the output (STDERR) of the variants that are obtained when the option '-p' is used in:
vcfutils.pl varFilter -p [file_with_the_filtered_out_variants]
?
An example of this output (4 rejected variants, with field-1 values "P", "G", "g" and "a", respectively) is:
P chr01 4572 . G T 225 . DP=194;VDB=0.0000;AF1=0.5;AC1=1;DP4=80,82,25,7;MQ=60;FQ=225;PV4=0.0033,1,1,1.5e-05 GT:PL:GQ 0/1:255,0,255:99
G chr01 6691 . T A 13.2 . DP=43;VDB=0.0000;AF1=0.5;AC1=1;DP4=20,20,2,1;MQ=60;FQ=16.1;PV4=1,0.13,1,0.00065 GT:PL:GQ 0/1:43,0,255:46
g chr01 69870 . GTTTTTTTTTTTTT GTTTTTTTTTTTT,GTTTTTTTTTTT 66.5 . INDEL;DP=572;VDB=0.0367;AF1=1;AC1=2;DP4=0,7,14,165;MQ=60;FQ=-290;PV4=1,1,1,1 GT:PL:GQ 1/1:107,255,0,110,255,98:99
a chr01 115171 . C A 6.98 . DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=36;FQ=-30 GT:PL:GQ 1/1:36,3,0:4
By inspecting the source of vcfutils.pl it seems that the possible values are these letters: "UQdDaGgPMS". I suppose that each letter is a different reason for filtering out the variant but I do not know the meaning of each one.
Thank you in advance
Rafael
Good explanation although it is still not clear the meaning of the tags "U", "M" and "S" (if they really exist). "M" = "MAPQ bias"?. I had already queried the documentation of samtools you cite and made varFilter -h but I do not see the answer there. Thank you so much for your time, ashutoshmits.