Hello there
I have a issue with sam SNP calling. I work with captured genomic sequences.
The fold coverage is very high at 600X. I used BWA (mismatch penalty -7) to map the reads to the genome and used samtools to call SNPs. I used mpileup and then realised that a known SNP was not called by mpileup and I tried to investigate what is happening in that region with pileup. The output is as follows
What I do not understand is why is samtools not reporting the consensus sequence as K ? Is this the reason why it is not called as variant position ?
Thanks a lot for the answers
I have a issue with sam SNP calling. I work with captured genomic sequences.
The fold coverage is very high at 600X. I used BWA (mismatch penalty -7) to map the reads to the genome and used samtools to call SNPs. I used mpileup and then realised that a known SNP was not called by mpileup and I tried to investigate what is happening in that region with pileup. The output is as follows
CFA15 1299612 T T 255 0 59 309 g,GG,,.g,,.G.g.,,,gg.G,gg,g,,.G.,,,,,,GG...gGG,,,g.ggggg,.ggG.gg..g,Gg.Gggg.G
.g,,.gg,,,,gg.,g,g.,,.Gg,.,gg,gg,ggggG,..Ggg,,g,g,,,.g,gG,gGgg.g,GG,Gg,,..,,g.G,,,,,,,.G,,gg,gG.gg,gGGGg.GGGG,g,gGg,G,,g,,g,.,g,g..GG.G.,gggg
GggG.G,,g,g,.,,..,gGG..G,G,,..g,gg,g,.,Ggg,.G,g,.,gGGGGg,G.GGg,.gggG,g,,,g,G.G..G...,g^]g^],^],^]g^]G !T!!]^^!^^^!^!^^^^!!^!^!!^!^^^!^^^^^^
^!!^^^!!!^^^!^!!!!!^^!!!^!!^^!^!!^!!!!^!^!^^^!!^^^^!!^^!^!^^^^!!^^^!!^!!^!!!!!^^^!!!^^!^!^^^^!^!!^!!!!^!^!!^!!^^^^^^!^!^^^^^^^^!^^!!^!!^!!^!!
!!!^!!!!^!^!!!^!^^!^^!^^^!^!^^!!^!^^!!!!!!!!^!^^!]!^^^^^^^!!!^^!^!^^^B!^!!^!^^^!!!^^!^!^^^!!!!,!^!^!!!^^!!!!^!^__!_!_!EE!EEA>!!EE!!
.g,,.gg,,,,gg.,g,g.,,.Gg,.,gg,gg,ggggG,..Ggg,,g,g,,,.g,gG,gGgg.g,GG,Gg,,..,,g.G,,,,,,,.G,,gg,gG.gg,gGGGg.GGGG,g,gGg,G,,g,,g,.,g,g..GG.G.,gggg
GggG.G,,g,g,.,,..,gGG..G,G,,..g,gg,g,.,Ggg,.G,g,.,gGGGGg,G.GGg,.gggG,g,,,g,G.G..G...,g^]g^],^],^]g^]G !T!!]^^!^^^!^!^^^^!!^!^!!^!^^^!^^^^^^
^!!^^^!!!^^^!^!!!!!^^!!!^!!^^!^!!^!!!!^!^!^^^!!^^^^!!^^!^!^^^^!!^^^!!^!!^!!!!!^^^!!!^^!^!^^^^!^!!^!!!!^!^!!^!!^^^^^^!^!^^^^^^^^!^^!!^!!^!!^!!
!!!^!!!!^!^!!!^!^^!^^!^^^!^!^^!!^!^^!!!!!!!!^!^^!]!^^^^^^^!!!^^!^!^^^B!^!!^!^^^!!!^^!^!^^^!!!!,!^!^!!!^^!!!!^!^__!_!_!EE!EEA>!!EE!!
Thanks a lot for the answers
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