A question appears when working with vcf file produced by UnifiedGenotyper on multiple samples. It is of course better to work with single sample vcf file so I was trying to split the multiple sampel vcf file. I used vcf-subset of vcftools but the problem is that the splitted single sample vcf file still has homozygous reference calls. Does anyone has a easy solution to this problem?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Have you tried the -e parameter? I suppose -a should also be used to get rid of alternate alleles not found in the subset.
Here is the usage of vcf-subset:
Usage: vcf-subset [OPTIONS] in.vcf.gz > out.vcf
Options:
-a, --trim-alt-alleles Remove alternate alleles if not found in the subset
-c, --columns <string> File or comma-separated list of columns to keep in the vcf file. If file, one column per row
-e, --exclude-ref Exclude rows not containing variants.
-f, --force Proceed anyway even if VCF does not contain some of the samples.
-p, --private Print only rows where only the subset columns carry an alternate allele.
-r, --replace-with-ref Replace the excluded types with reference allele instead of dot.
-t, --type <list> Comma-separated list of variant types to include: SNPs,indels.
-u, --keep-uncalled Do not exclude rows without calls.
-h, -?, --help This help message.
-
If you want to Split Large sized VCF Files of Vcards into Smaller ones, then you can try our most efficient VCF Splitter Tool. The utility can easily divide the VCF files with all the contacts and other files without any data loss. If you want to Split Large sized VCF Files of vCard into Smaller ones, then you can try our most efficient VCF Splitter Tool.
Visit at : https://www.osttopstapp.com/split-vcf.html
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
31 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
32 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment