SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
VCF file - 'X' bases in the ALT position and QUAL = 0 . Why ? north_zeb Bioinformatics 3 12-04-2014 01:58 PM
Why my variant is found if AD alt = 0 in my vcf file ? Sam64 Bioinformatics 2 07-03-2014 06:40 AM
VCF - genotypes - "missing alleles" Elsie Bioinformatics 2 02-10-2013 01:08 PM
VCF file - no ALT but DP4 alternative exist Rachelly Bioinformatics 2 04-04-2012 02:12 AM
VCF file, missing AA, AC and AN tags phatjoe Bioinformatics 0 01-15-2012 04:17 PM

Reply
 
Thread Tools
Old 07-30-2021, 05:14 AM   #1
A.R.T
Junior Member
 
Location: Leiden

Join Date: Jul 2021
Posts: 2
Default Missing value in ALT alleles for VCF file

Hi
I am working on my VCF files (mapped to GRCh37) which contains some missing values in ALT allele site. While there is (.) instead of allele name, the REF allele and variant rs_number in addition to other details are provided. Would you please let me know how can I fix it? Is there any special tool for retrieving missing variants in VCF?

example:

chr22 42523943 rs16947 A .
A.R.T is offline   Reply With Quote
Old 08-04-2021, 10:34 PM   #2
dcameron
Member
 
Location: Australia

Join Date: Mar 2013
Posts: 27
Default

It's likely that your coverage at that position is too low for the variant caller to make any call.

> Would you please let me know how can I fix it?

Verify that these variants are indeed called as MISSING due to insufficient coverage. If this is indeed the case, you need to sequence more, or explicitly handle missing variants in your pipeline.
dcameron is offline   Reply With Quote
Old 08-27-2021, 01:54 AM   #3
A.R.T
Junior Member
 
Location: Leiden

Join Date: Jul 2021
Posts: 2
Default

Quote:
Originally Posted by dcameron View Post
It's likely that your coverage at that position is too low for the variant caller to make any call.

> Would you please let me know how can I fix it?

Verify that these variants are indeed called as MISSING due to insufficient coverage. If this is indeed the case, you need to sequence more, or explicitly handle missing variants in your pipeline.


Thank you @dcameron. I noticed that missing positions appeared after I did genome liftover by NCBI tool (https://www.ncbi.nlm.nih.gov/genome/tools/remap). So, my original VCFs do not contain any missing variant. I think I have to choose another tool for converting my GRCh38 vcfs to GRCh37.
A.R.T is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:15 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO