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
A Genetic Genealogy Community
Y-DNA, Mt-DNA, Autosomal DNA
Y-DNA, Mt-DNA, Autosomal DNA
Variant Call Files
3 posts
• Page 1 of 1
![]()
Posts: 9
Joined: Tue Mar 27, 2012 2:00 pm YDNA: R1b-Z196-Z220* MtDNA: T1a1 |
|
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 I have already extracted the chrY part for a newer version of this file (2141 samples) and it is at https://www.box.com/s/c18dfed612544ef28fec .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:
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 |
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 |
3 posts
• Page 1 of 1
Who is online
Users browsing this forum: No registered users and 1 guest