Hello,
I'm running into an error trying to parse the PL from my VCF using snp2h5 to get the gene_probs.h5 file. The error seems to indicate that PL isn't in my VCF.
ERROR: vcf.c:504: VCF format string does not specify GL, GP, or PL token so cannot obtain genotype probabilities. Format string: 'GT'.
However, PL is clearly in the format string. This is the head of my VCF:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 5397-JL-0001 5397-JL-0002
chr1 11863 . C A 95.27 PASS . GT:PL 0|1:129,0,347 0|1:118,0,72
chr1 12198 . G C 355.27 PASS . GT:PL 0|1:455,0,496 1|1:312,27,0
chr1 12383 . G A 364.77 PASS . GT:PL 0|1:516,0,684 1|0:270,0,52
chr1 12719 . G C 50.77 PASS . GT:PL 0|1:79,0,391 0|0:0,12,168
Do you have any suggestions to get this to run? Thanks
Hello,
I'm running into an error trying to parse the PL from my VCF using snp2h5 to get the gene_probs.h5 file. The error seems to indicate that PL isn't in my VCF.
ERROR: vcf.c:504: VCF format string does not specify GL, GP, or PL token so cannot obtain genotype probabilities. Format string: 'GT'.However, PL is clearly in the format string. This is the head of my VCF:
Do you have any suggestions to get this to run? Thanks