Extract VCF of tumor variants from a list of SNPs

I have a list of germline SNPs. I want to get the read level information, etc. of these SNPs in the tumor BAM file and format it into a VCF (ie. to see the read level support for the germline SNPs in the tumor sample). Is there an easy way to do this?

mutect2 snp

• 718 views • link

written 5.5 years ago by vctrm67 •

0 answers

No answers yet.

More posts like this

How to annotate the snps we get after GWAS?
written 5.7 years ago by biotechnology415 •

I did gwas on a plant data. As you know after running gwas model, we can get some peak snps. As the results of gwas …
Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
written 5.9 years ago by vctrm67 •

To my understanding, one needs the B-allele frequencies for allele-specific copy number. To get those, you usually use germline SNPs for the following reason: "In …
Calling CNVs using a single tumor sample
written 5.9 years ago by vctrm67 •

If I only have a tumor sample to call CNVs from, is it possible to exclusively call somatic or germline CNVs? It seems to me …
bcftools isec question?
written 6.2 years ago by vctrm67 •

How does bcftools isec work, ie. which parameters does it intersect on? I was assuming chromosome, position, ref, and alt alleles only, and disregards any …
Calling germline SNPs using GATK HaplotypeCaller in a single sample
written 6.3 years ago by vctrm67 •

I am using GATK 4.1.2.0. What is the best way to call germline variants from single samples? I have a cohort of samples and want …
GATK BaseRecalibrator and platform?
written 6.6 years ago by vctrm67 •

Posting here because the GATK forums are slow to respond. To my understanding, BaseRecalibrator requires certain fields, of which includes the platform information. I received …
Combining two VCFs each with own set of mutations
written 6.8 years ago by vctrm67 •

I have two VCF files, each containing somatic mutation calls on each chromosome (ie. the VCFs are not separated by chromosome number or mutation position …
Multi samples (Normal and Tumor) somatic SNPs identification
written 6.9 years ago by Omics data mining

Hi everyone I have bam files of multiples normal and tumor samples. For the efficient SNPs prediction, Its recommended to have merged multi sample vcf …
Running Oncotator with MuTect2 output
written 9.6 years ago by haiying.kong

I got somatic mutation list with MuTect2, and it is in vcf format. The last 2 columns in the vcf file are for tumor sample …
How to Prepare Input Files for VerifyBamID?
written 10.2 years ago by haiying.kong

The usage of the software is: verifyBamID --vcf [input.vcf] --bam [input.bam] --out [output.prefix] --verbose --ignoreRG I am reading the manual, but it is still not …