Collect GQ values from gvcf file using vcftools

Can someone please let me know how can i use VCFtools to collect collect GQ values from gvcf.gz files. Thanks

next-gen sequencing

• 1,256 views • link

written 7.2 years ago by jalinir 0

What have you tried? Have you looked at bcftools?

• 0 views • link

written 7.2 years ago by Ram 4.5K

1 answer

i tried vcf tools and i think i got it. thanks.

• 0 views • link

written 7.2 years ago by jalinir 0

More posts like this

Regarding opening of fastq whole genome data file and its assembly
written 4.2 years ago by Shakunthala Natarajan 5

1. I have two 3.7 GB whole genome data files (read 1 and read 2) of whole genome data obtained by paired end sequencing in …
Genebank flat file
written 5.9 years ago by yakhouba.kane3 0

Hi, does someone know how to open GeneBank or GenPet fat files? I have tried with the tools i have but any success. Please let …
Homolog gene in different organisms
written 6.3 years ago by RE 0

Hi It is first time for me to know about finding homolog gene. I would like to know if someone know how can i found …
Refseq accessions - getting gene function and GO terms for each one
written 7.8 years ago by Biogeek 48

Can someone please let me know how I can get access to refseq gene names/functions and GO (CC,BP,MF) information for each gene using information gained …
SNPs in population; vcftools
written 9.0 years ago by DanielC 21

Dear ALL, I have been looking for a way to find "which nsSNP (with rs ID number like rs769971095) belong to what population(s), and if …
Simulated data for Structural Variants
written 9.5 years ago by Chan 4

Hi everyone, since I am new to Structural Variants, could someone please let me know how can I get access to the simulated data for …
Cygwin installation on windows 10
written 10.2 years ago by verma 3

Anyone can please tell me how to get the Cygwin on windows 10 operating system. Also please let me know the link from where I …
Chimeric reads identification and removal
written 10.4 years ago by lakhujanivijay 594

I am thinking to use "identify_chimeric_seqs.py" from QIIME package (method - blast_fragments) for chimeric reads removal. Can someone let me know where can I find …
Help needed parsing VCF files
written 12.3 years ago by devenvyas 77

Hello, I need to collect a set of ~330,000 SNPs from a set of extended-VCF files (available [here][1] and [here][2]). The only information I have …
not able to get the actual information of VCF file from vcf-stats
written 12.4 years ago by aloksinghpawar1802 0

Hi all, I am not able to get the information from vcftools-stats tools,please let me know how to get the output in the tabular format …