vcfverifier
| Crates.io | vcfverifier |
| lib.rs | vcfverifier |
| version | 0.1.1 |
| source | src |
| created_at | 2022-07-30 22:24:41.141161 |
| updated_at | 2022-07-30 22:27:41.838741 |
| description | Verifies that a given VCF matches a given FASTA by comparing the REF column in the VCF to the underlying FASTA sequences |
| homepage | |
| repository | https://github.com/cmdcolin/vcfverifier |
| max_upload_size | |
| id | 635808 |
| size | 94,951 |
Colin Diesh (cmdcolin)
documentation
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