SNP associated contigs
I am using usegalaxy.org for SNP analysis. After mapping with bowtie2 I got BAM file including QNAME FLAG RNAME POS and on variant calling I got Chrom Pos ID Ref Alt. Showing Variant position on reference genome. I want to get those sequences associated to SNP. Could any one please tell me how to get this info???????
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aabhordia •
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It is not clear to me what you want, can you elaborate?
As I am mapping my query against reference genome, and as a result I got file containing ID of query and reference name and position where it has mapped. When I do variant calling it showed me reference chr ID, position, REF, ALT. I want to get those sequences of query that has SNP (showing after variant calling). Or is there anything which I am doing or asking in wrong way. Please suggest me.