amend chromosome format

Question

[Nance]

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!

[Pierre Lindenbaum]

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.

[Nance]

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?

[Pierre Lindenbaum]

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.

[Nance]

Thank you very much for your assistance!