Variant Call Files

Moderators: Rootsy, GregRM


Posts: 9
Joined: Tue Mar 27, 2012 2:00 pm

YDNA:
R1b-Z196-Z220*
MtDNA:
T1a1
PostPosted: Thu Dec 27, 2012 8:27 am
How can I extract with bcftools view only the Y variant calls in the ftp://ftp-trace.ncbi.nih.gov/1000genome ... b37.vcf.gz variant call file.
Or is these Y variants the same as the ones in the ALL.chrY.phase1_samtools_si.20101123.snps.low_coverage.genotypes.vcf.gz file?
This works with samtools view and bam files.
Hans

Posts: 3
Joined: Fri Nov 09, 2012 12:56 am

YDNA:
R1b-Z343
MtDNA:
H3 (T152C)
PostPosted: Sat Dec 29, 2012 11:07 pm
Hi Hans,
The first file you linked to is from an Omni genotyping microarray/"chip" similar to that used by 23andMe and FTDNA Family Finder.

I have already extracted the chrY part for a newer version of this file (2141 samples) and it is at https://www.box.com/s/c18dfed612544ef28fec . (I think I may have a version of the older file extracted, but I assume you prefer the newer version.

I do the extraction on Linux with commands like the following:
Code: Select all
grep # sourceFilename.vcf > destFilename.vcf
grep -w Y sourceFilename.vcf >> destFilename.vcf

The first command extracts the header comments and the second appends the chrY variant data to the file.

I wouldn't know if or how bcftools could be used to do such extraction.

Greg

Posts: 9
Joined: Tue Mar 27, 2012 2:00 pm

YDNA:
R1b-Z196-Z220*
MtDNA:
T1a1
PostPosted: Fri Jan 04, 2013 7:54 pm
Thanks Greg.

I completely forget about the Grep command.
I certainly will use your dropbox file.
The vcf I mentioned only contained 526 Y chromosome samples.

If you do not mind I will be back with more questions.
To get some more experience with the 1000 genomes samples a worked on the Z220+ samples with samtools. mpilup, bcftools etc.
In the end of Januari I expect my WGS from DNA DTC; I like to be prepared but above all to find more SNPs in at least the Z209 downstream branche.

Hans

Return to 1K Genomes Project

Who is online

Users browsing this forum: No registered users and 1 guest

cron