amend chromosome format

0

Entering edit mode

2.7 years ago

Nance ▴ 10

Hi,

I have genetic data and the chromosones [chr] are in the dbsnp format [latest vcf hg38 version downloaded from https://ftp.ncbi.nih.gov/snp/latest_release/VCF/]

>     Chr
>     NW_003315915.1
>     NW_003315922.2
>     NW_003871060.2
>     NW_018654722.1
>     NW_021160015.1
>     NT_167249.2

Does anyone know how I amend these in to chr xx' format? I.E chr01 chr02 ... etc

Thanks!

gene dbsnp chr • 840 views

ADD COMMENT • link 2.7 years ago by Nance ▴ 10

1

Entering edit mode

see "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_assembly_report.txt" (from https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39 ) . These are ALT_REF_LOCI, so I don't think you can just replace it with the chromosome number.

ADD REPLY • link 2.7 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

Thank you for your help. Do you know why this is / why they aren't mapped to chromosomes / do you have any ideas of how this could be done?

ADD REPLY • link 2.7 years ago by Nance ▴ 10

1

Entering edit mode

why they aren't mapped to chromosomes

google: https://gatk.broadinstitute.org/hc/en-us/articles/360041155232-Reference-Genome-Components

Alternate contigs, alternate scaffolds or alternate loci allow for representation of diverging haplotypes. These regions are too complex for a single representation. Identify ALT contigs by their _alt suffix. The GRCh38 ALT contigs total 109Mb in length and span 60Mb of the primary assembly. Alternate contig sequences can be novel to highly diverged or nearly identical to corresponding primary assembly sequence.