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Spanning deletion is not identified as an indel

Open stevendavis opened this issue 7 years ago • 0 comments

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?

stevendavis avatar May 23 '18 18:05 stevendavis