https://github.com/cmdcolin/vcfverifier

Check that a VCF matches a given reference genome
https://github.com/cmdcolin/vcfverifier

Last synced: 4 days ago
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Check that a VCF matches a given reference genome

• Host: GitHub
• URL: https://github.com/cmdcolin/vcfverifier
• Owner: cmdcolin
• License: mit
• Created: 2022-07-29T23:50:35.000Z (over 2 years ago)
• Default Branch: master
• Last Pushed: 2024-07-29T16:29:19.000Z (4 months ago)
• Last Synced: 2024-10-31T11:57:12.180Z (19 days ago)
• Language: Rust
• Size: 41 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# vcfverifier

Checks that a given VCF file matches a given assembly in FASTA format by

checking that the REF column matches the FASTA file for each record in the

FASTA file (case insensitive)

## Install

First install rust, probably with rustup https://rustup.rs/

Then

```

cargo install vcfverifier

```

## Usage

```

## Generated FASTA index (fai)

samtools faidx myfile.fa

## Run the verifier

vcfverifier --fasta myfile.fa --vcf myfile.vcf.gz

```

Allows plaintext, gzip, or bgzip vcf files as input to the --vcf flag

## Approx speed

Processing chr1 (6.5M rows) of the 1000 genomes dataset takes ~24seconds

```

$ time vcfverifier --fasta hs37d5.fa --vcf ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

Lines processed: 6468347

No mismatching lines found

vcfverifier --fasta ~/Downloads/hs37d5.fa --vcf   24.07s user 0.26s system 99% cpu 24.330 total

```

## Note

My first rust project!

Uses faimm to memory-map the indexed FASTA file, keeping memory usage low (the

entire FASTA does not have to be loaded into memory and the VCF is read line by

line) https://github.com/veldsla/faimm