compare samples

jgSoton · 09-29-2011, 08:34 AM

Anyone know a quick way to compare two samples that have undergone exome-sequencing?

I seem to have two samples that have very similar variant call and I wonder if it is actually the same individual. -I have sam and bam files. I have an edited version of the variant call but not the raw vcf files and the moment.

thanks,
Jane

sdvie · 09-30-2011, 02:08 AM

Hi Jane,

In case you can get hold of the raw vcf files, you can go for this:
GATK Combine Variants
using set=Intersection to obtain the intersection of variant positions in two files

Otherwise, you could call the variants again using your bam files as input for the GATK Unified Genotyper.

cheers,
Sophia

jgSoton · 10-03-2011, 01:38 AM

Hi,

Thanks Sophia. I guessed I would need the vcf files really so I am remaking them. I will try the GATK option you suggest, and I think I will try vcftools to compare files too.

Cheers,
Jane

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09-29-2011, 08:34 AM	#1
jgSoton Member Location: UK Join Date: Sep 2011 Posts: 12	compare samples Anyone know a quick way to compare two samples that have undergone exome-sequencing? I seem to have two samples that have very similar variant call and I wonder if it is actually the same individual. -I have sam and bam files. I have an edited version of the variant call but not the raw vcf files and the moment. thanks, Jane

09-30-2011, 02:08 AM	#2
sdvie Member Location: Spain Join Date: Jul 2010 Posts: 68	Hi Jane, In case you can get hold of the raw vcf files, you can go for this: GATK Combine Variants using set=Intersection to obtain the intersection of variant positions in two files Otherwise, you could call the variants again using your bam files as input for the GATK Unified Genotyper. cheers, Sophia

10-03-2011, 01:38 AM	#3
jgSoton Member Location: UK Join Date: Sep 2011 Posts: 12	Hi, Thanks Sophia. I guessed I would need the vcf files really so I am remaking them. I will try the GATK option you suggest, and I think I will try vcftools to compare files too. Cheers, Jane