Question: DiscoSNP++ 2.2.X VCF calls a A to an A SNP
1
gravatar for laeb
7 weeks ago by
laeb50
laeb50 wrote:

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?

discosnp • 169 views
ADD COMMENTlink modified 6 days ago by pierre.peterlongo600 • written 7 weeks ago by laeb50
0
gravatar for miguel
7 weeks ago by
miguel0
miguel0 wrote:

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

ADD COMMENTlink written 7 weeks ago by miguel0
0
gravatar for Beuss
6 weeks ago by
Beuss40
France
Beuss40 wrote:

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

ADD COMMENTlink written 6 weeks ago by Beuss40
0
gravatar for pierre.peterlongo
23 days ago by
France
pierre.peterlongo600 wrote:

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

ADD COMMENTlink written 23 days ago by pierre.peterlongo600

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

ADD REPLYlink written 23 days ago by laeb50

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

ADD REPLYlink written 10 days ago by pierre.peterlongo600
0
gravatar for pierre.peterlongo
6 days ago by
France
pierre.peterlongo600 wrote:

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

ADD COMMENTlink written 6 days ago by pierre.peterlongo600

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

ADD REPLYlink written 6 days ago by laeb50
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