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rqtl / qtl2

QTL analysis software for high-dimensional data and complex cross designs
https://kbroman.org/qtl2
GNU General Public License v3.0
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convert vcf file of an haploid to run r/qtl or r/qtl2 #205

Closed jeancarlier34 closed 2 years ago

jeancarlier34 commented 2 years ago

Hello,

I work on an haploid fungus. I have SNP data in a vcf from a cross between 2 strains that I would like to use to construct a genetic map using r/qtl. What are the functions I could used to convert the vcf (encoded for an haploid, see below a sample of the first line)?

scaffold_1 316761 . T G 24186.3 . AC=90;AF=0.486;AN=185;BaseQRankSum=0.00;DP=2570;FS=0.000;MLEAC=92;MLEAF=0.497;MQ=59.69;MQRankSum=0.00;QD=33.50;ReadPosRankSum=0.00;SOR=0.264 GT:AD:DP:GQ:PL 1:0,4:4:99:99,0 0:4,0:4:99:0,99 1:0,5:5:99:144,0

Many thanks, Jean

kbroman commented 2 years ago

There are no particular functions for converting vcf files to R/qtl2 format, but see vcftools or the vcfR package and this discussion at the R/qtl2 google group.