What is the name of this build What is equivalent to build37.fa.bz2

Question

[Daisy]

Hi everyone

So sorry if it is a naiive thing, but I am still new: What is name of this build:

ftp://ftp.completegenomics.com/ReferenceFiles/build37.fa.bz2

I try to use https://www.ncbi.nlm.nih.gov/genome/tools/remap#tab=asm to remap to hg19 or hg38 for annovar but there is no build37.1 in the options available.

This is what is found in the vcf header:

##source_GENOME_REFERENCE=NCBI build 37
##source_GENE_ANNOTATIONS=NCBI build 37.1
##source_DBSNP_BUILD=dbSNP build 132
##source_COSMIC=COSMIC v48
##reference=ftp://ftp.completegenomics.com/ReferenceFiles/build37.fa.bz2

I feel I miss something naiive here that is causing this confusion. thanks

Answer 1

[finswimmer]

Hello Daisy,

NCBI build 37 is equivalent to hg19 if we are talking about human.

fin swimmer

[Daisy]

Yes human, thanks finswimmer. So I don't need any conversion to hg19 then :)

[finswimmer]

Correct.

Please mark my answer as accepted if this is your solution.

fin swimmer

Answer 2

[Sumanth]

This isn't completely accurate as, according to the Complete Genomics CGATools User Guide (page 16), their "build37.fa.bz2" deviates from NCBI build 37/hg19 by replacing chrM with NC_012920.1.

Here's Dockerfile that'll build the equivalent file for you: https://github.com/peddamat/cgatools-build37-fa

For the moment, please ignore the README.md.