Extracting single chromosome from WGS cram/bam files before downloading

Question

[berndmann]

For a study of VNTR copies I'm looking for high-coverage public-accessible WGS data such as 1KG,HGDP and SGDP. Since downloading the whole cram file if one just needs one chromosome can take a long time, I wonder if it is possible to subset the cram file to a single-chromosome bam file and just download this part of the data. If that is not possible I would like to ask for the fastest way to achieve this. Worst case would be download the whole file and subset locally but I would like to avoid this.

Best, Bernd

Answer 1

[GenoMax]

See: https://www.internationalgenome.org/faq/how-do-i-get-a-genomic-region-sub-section-of-your-files/

[berndmann]

Great. Fantastic that samtools supports streaming remote files!

[berndmann]

bernd:~$ samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455
[E::hts_open_format] Failed to open file "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam" : Protocol not supported
samtools view: failed to open "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam" for reading: Protocol not supported
bernd:~$ samtools --help

Program: samtools (Tools for alignments in the SAM format)
Version: 1.13 (using htslib 1.13+ds)

Usage:   samtools <command> [options]

When I try to run the example from their webpage it fails with "Protocol not supported"

[GenoMax]

Make sure you are using a newer version of samtools. Works with v.1.21 which is the latest. Your samtools is from 2021.

[berndmann]

So it looks like it was just the samtools version. Thanks for the hint.

Subsetting a streamed cram file still seems to take a very long time on my end.

I do this: samtools view ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239482/NA12775.final.cram -r chrX --reference GRCh38_full_analysis_set_plus_decoy_hla.fa

This already runs for roughly 20 minutes. I would assume this should be done in less than 10?

`

[Pierre Lindenbaum]

wrong parameter.

-r, --read-group STR ...are in read group STR

you want

 samtools view ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239482/NA12775.final.cram  chrX --reference GRCh38_full_analysis_set_plus_decoy_hla.fa

[Pierre Lindenbaum]

use 'https://' instead of 'ftp://'