#25 Drosophila chromosome encoding

[William Gilks]

Hi, I was wondering if you could all function for Drosophila melanogaster.

vcftools 0.1.2b converting vcf to plink for D.melanogaster causes problems, due to strange chromosome names. Any chance you could add function to include them?

Cheers,

Will

Output error message:
Unrecognized values used for CHROM: YHet - Replacing with 0.
PLINK: Only outputting biallelic loci.
Unrecognized values used for CHROM: dmel_mitochondrion_genome - Replacing with 0.
Unrecognized values used for CHROM: 2L - Replacing with 0.

Chromosome ID's for D.melanogaster assembly v5.9 are:
YHet
dmel_mitochondrion_genome
2L
X
3L
4
2R
3R
Uextra
RHet
2LHet
3LHet
3RHet
U
XHet

[Anthony Marcketta]

Will,

I have just committed a new change to the developmental version (v0.1.13) that will allow a user to specify a tab-delimited file containing a map of chromosome name to integer value for the --plink and --plink-tped functions.

Please download and make the developmental version of vcftools and try out this functionality. Let me know if you have any further questions.