Hi ,
I have two VCF files that belongs to disease samples and four VCF files that generated from normal samples. Now I would to filter of SNPs . I would like to get the SNPs that are present in only disease group so that I can go further to validate them by other methods. Is there any tool that does this kind of analysis?
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written
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GouthamAtla
I would start with vcftools merge command and then write a script to remove variants that are present in controls. Maybe there is an existing tool that will filter by genotype call in certain samples, but I am not aware of one.
If the disease you're looking at is rare, I would also consider filtering by 1000 genomes or NHLBI allele frequencies.
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written
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Katie D'Aco
Thank you for the reply. I have used multisample SNP calling ( UnifiedGenotyper ) and filtered SNPs and selected SNPs with AWK.
You can start with GATK CombineVariants to merge all the VCFs at once.
Then use GATK SelectVariants to filter out variants that occur in only the two disease samples.
Thank you for the reply. I have used multisample SNP calling ( UnifiedGenotyper ) and filtered SNPs and selected SNPs with AWK.
Hi Goutham,
My requirement is also some what similar to yours. I have to find snps which are present in affected but not in unaffected samples, then I have to prepare a list For example,
Samples 4:1243-SNV 5:1277-SNV 15:4070-SNV ..... ..... ...... ...... ..... ..... 16:5335-SNV
A(affected) C_T A_G A_T ..... ..... ...... ...... ..... ..... A_C
B(unaffected) C_C A_A A_A ..... ..... ...... ...... ..... ..... A_A
C(affected) C_T A_G A_T ..... ..... ...... ...... ..... ..... A_C
D(affected) C_T A_G A_T ..... ..... ...... ...... ..... ..... A_C
Any help :)
Cheers,
Ram
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written
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ramanandan.prabhakaran •
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