I'm currently working with a VCF file that contains this row (for example; header included):
Now, I'm wondering, is it valid for the PL data column to stick out on its own? Shouldn't it be together in the previous column, semicolon-separated from other INFO values?
I'm only wondering because I've been trying to feed the VCF file to a filtering script, and the script seems to stumble on this oddity. If the row is indeed invalid, I'm going to try fix the initial pipeline that produced the VCF file. If not, then it's the script that needs fixing.
Thanks in advance .
Code:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT - chr1 761958 . C T 67 . DP=39;VDB=0.0274;AF1=0.5;AC1=1;DP4=18,0,20,1;MQ=36;FQ=47;PV4=1,7.9e-17,1,1 PL 97,0,74
I'm only wondering because I've been trying to feed the VCF file to a filtering script, and the script seems to stumble on this oddity. If the row is indeed invalid, I'm going to try fix the initial pipeline that produced the VCF file. If not, then it's the script that needs fixing.
Thanks in advance .
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