SNP associated contigs

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2.9 years ago

aabhordia ▴ 30

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???????

SNP associated contig • 873 views

ADD COMMENT • link 2.9 years ago by aabhordia ▴ 30

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I want to get those sequences associated to SNP

It is not clear to me what you want, can you elaborate?

ADD REPLY • link 2.9 years ago by WouterDeCoster 47k

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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.

ADD REPLY • link 2.9 years ago by aabhordia ▴ 30

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