User: laeb

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laeb60
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l***@biosustain.dtu.dk

Posts by laeb

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Detecting gene insertions with DiscoSNP
... Hi, We have 2 bacterial strains. Parent and child. We have inserted a gene in the child strain. When we run discoSNP on reseq data of those 2 strains it only finds a single SNP difference. We have mapped raw reads to the plasmid we used to insert the gene and verified that the gene is indeed present ...
variant calling discosnp written 3 months ago by laeb60 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: DiscoSNP++ 2.2.X VCF calls a A to an A SNP
... Thanks. I will try the commit and see if it solves the issue. Again thank you for a great tool. ...
written 5 months ago by laeb60
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Comment: C: DiscoSNP++ 2.2.X VCF calls a A to an A SNP
... 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 taatgcagtgggcattatcgatgatgtaaccattcacacaggttatttagcttttgatccttgaaccattaattaacCCAGAAATAGAAATTAC ...
written 6 months ago by laeb60
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DiscoSNP++ 2.2.X VCF calls a A to an A SNP
... 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 ...
discosnp written 7 months ago by laeb60 • updated 5 months ago by pierre.peterlongo660

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