PyVCF
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Spanning deletion is not identified as an indel
Not sure if this is a bug or a misunderstanding on my part. Consider these example VCF records:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
chrom 100 . A * . PASS . GT:FT 1/1:PASS
chrom 200 . A *,G . PASS . GT:FT 1/2:PASS
I expected both the examples to be identified as indels, but in both cases, _Record.is_indel() returns false.
At position 100, there is only one ALT allele, a spanning deletion. I expected: _Record.is_indel() == true _Record.is_snp() == false
At position 200, there are two ALT alleles, a deletion, and a snp. I expected: _Record.is_indel() == true _Record.is_snp() == true
What am I missing here?