DiscoSNP++ 2.2.X VCF calls a A to an A SNP

Question

[laeb]

I also posted you your github issues. Basically the VCF has a this line:

NC_001136.10 410323 1755 A A . PASS Ty=SNP;Rk=0.073173;UL=77;UR=471;CL=.;CR=.;Genome=A;Sd=1 GT:DP:PL:AD:HQ 0/1:167:1138,17,1238:86,81:68,67 0/1:172:1427,21,1028:76,96:67,68

If I am interpreting that correctly then thats a SNP where REF is A and ALT is also A. Why is that called as SNP?

Answer 1

[miguel]

Same issue here, the resulting VCF will still pass VCF validation, but causes issues when you try to run an index

Answer 2

[Beuss]

Same issue here also. Some explanations would be appreciate. Thanks.

Answer 3

[pierre.peterlongo]

Hello all, Sorry for this very late answer.

This is a strange unknown behaviour. Laeb, would you mind finding this variant in the ..._coherent.fa file (finding the variant id 410323) and showing this here so we could understand the issue?

Pierre

[laeb]

I believe its these two lines:

SNP_higher_path_1755|P_1:108_A/T|high|nb_pol_1|left_unitig_length_77|right_unitig_length_471|C1_86|C2_76|Q1_68|Q2_67|G1_0/1:1138,17,1238|G2_0/1:1427,21,1028|rank_0.073173 taatgcagtgggcattatcgatgatgtaaccattcacacaggttatttagcttttgatccttgaaccattaattaacCCAGAAATAGAAATTACCCAAGTGGGGCTCTCCAACACAATGAGAGGAAAGGTGACTTTTTAAGGGTGCCAGACCCTGTTAAAAACCTTTGATGGCTATGTATTTTACAGTAAATTAAGTGCAAACATGTAAGTAAGCTTCTCAGTAAAAACCATACAAACATTGGGCGTGTGGCGTAGTCGGTAGCGCGCTCCCTTAGCATGGGAGAGGTCTCCGGttcgattccggactcgtccaaattattttttactttccgcggtgcggagatgcggacgtggccaactctgtctgccgtcgcaaaatgatttgaattttgcgtcgcgcacgtttctcatgtacatataataagtattttcatacagttctagcaagacgaggtggtcaaaatagaagcgtcctatgttttacagtacaagacagtccatactgaaatgacaacgtacttgacttttcagtattttctttttctcacagtctggttatttttgaaagcgcacgaaatatatgtaggcaagtattttctgagtctgctgacctctaaaattaatgctattgtgcaccttagtaacccaaggcaggacagttaccttgcgtggtgttactatggccggaagcccgaaagagttatcgttactccgattattttgtacagctgatgggaccttgccgtcttcattttttttttttt SNP_lower_path_1755|P_1:108_A/T|high|nb_pol_1|left_unitig_length_77|right_unitig_length_471|C1_81|C2_96|Q1_67|Q2_68|G1_0/1:1138,17,1238|G2_0/1:1427,21,1028|rank_0.073173 taatgcagtgggcattatcgatgatgtaaccattcacacaggttatttagcttttgatccttgaaccattaattaacCCAGAAATAGAAATTACCCAAGTGGGGCTCTCCAACACAATGAGAGGAAAGGTGACTTTTTAAGGGTGCCAGACCCTGTTAAAAACCTTTGATGGCTATGTATTTTACTGTAAATTAAGTGCAAACATGTAAGTAAGCTTCTCAGTAAAAACCATACAAACATTGGGCGTGTGGCGTAGTCGGTAGCGCGCTCCCTTAGCATGGGAGAGGTCTCCGGttcgattccggactcgtccaaattattttttactttccgcggtgcggagatgcggacgtggccaactctgtctgccgtcgcaaaatgatttgaattttgcgtcgcgcacgtttctcatgtacatataataagtattttcatacagttctagcaagacgaggtggtcaaaatagaagcgtcctatgttttacagtacaagacagtccatactgaaatgacaacgtacttgacttttcagtattttctttttctcacagtctggttatttttgaaagcgcacgaaatatatgtaggcaagtattttctgagtctgctgacctctaaaattaatgctattgtgcaccttagtaacccaaggcaggacagttaccttgcgtggtgttactatggccggaagcccgaaagagttatcgttactccgattattttgtacagctgatgggaccttgccgtcttcattttttttttttt

[pierre.peterlongo]

Thanks for the input. We are currently working on this issue. We keep you in touch as soon as we have news. Pierre

Answer 4

[pierre.peterlongo]

This issue was certainly due to a very rare case in which the two paths of a variant map the same locus but with very distinct alignment. A fix is proposed in the commit from today: 4dda977dd7f357557e9b91b5fecae71e8606fab0 https://github.com/GATB/DiscoSnp/commit/4dda977dd7f357557e9b91b5fecae71e8606fab0

Pierre

[laeb]

Thanks. I will try the commit and see if it solves the issue. Again thank you for a great tool.