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Heterogeneous Snp

i'm using bwa to mapping NGS data to reference, and want to find position with heterogeneous data: for example:

seq1 274 T 23  AAAAAAACCCCCCC    7<7;<;<<<<<<<<<=<;<;<<6

seq1 272 T 24  ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&
seq1 273 T 23  ,.....,,.,.,...,,,.,..A <<<;<<<<<<<<<3<=<<<;<<+
seq1 274 T 23  AAAAAAACCCCCCC    7<7;<;<<<<<<<<<=<;<;<<6
seq1 275 A 23  ,$....,,.,.,...,,,.,...^l.  <+;9*<<<<<<<<<=<<:;<<<<

are there some software can do this?

Thinks!!

snp
• 4,610 views • link
updated by brentp brentp • written by polangxin • polangxin

What are you asking? What is "heterogeneous data" in this context? Can you improve the formatting of your example, and maybe include the type of output you'd like to see (or some other explanation of the goal)?

• 242 views • link
written by matted matted

2 answers

I think you meant heterogeneous SNPs. You will have to use samtools to call for SNPs. The other tool is GATK unified genotyper. This link may help you: What is the best pipeline for human whole exome sequencing?

• 86 views • link
written by Ashutosh Pandey Ashutosh Pandey

Thank you！ i'll read the post you sugest. lol

• 0 views • link
written by polangxin • polangxin

Call the SNPs first with samtools or GATK and get the vcf file. Then you can extract the heterogenous SNPs using vcftools or just simple grep function. e.g. grep '0/1' from the vcf file which will exract all the eterogenous SNPS.

• 0 views • link
written by bioinfo bioinfo

Thank you! i've tried, and it works great!

• 0 views • link
written by polangxin • polangxin

You may need to be a bit careful about using 0/1 for heterozygotes. It is possible to have a more than two alleles present in some situations (more than one sample or if one sample has no reference allele). In those cases, you could get 0/2 or 1/2 or even 0/3, 1/3 or 2/3. These are unlikely but possible.

• 148 views • link
written by Sean Davis Sean Davis

Thank you! where can i read about the explaination of 0/1, 0/2? thanks again!

• 0 views • link
written by polangxin • polangxin

You'll want to read the VCF format specification.

• 0 views • link
written by Sean Davis Sean Davis

Thanks！ I'll read it carefully!

• 0 views • link
written by polangxin • polangxin

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