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

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I have already extracted the chrY part for a newer version of this file (2141 samples) and it is at https://www.box.com/s/c18dfed612544ef28fec .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

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