---
file_transformation: 
# Name hashes between GenBank: JJMO01_contigs and sequencing-center scaffold and chromosome names:
  vigra.VC1973A.gnm6.3nL8.scaff_name_hash.tsv corresponds with vigra.IA_panel.gwas.Sandhu_Singh_2020.JJMO01_contigs.tsv

hash_into_vcf_id.pl -vcf variants.filt.vcf -hash vigra.IA_panel.gwas.Sandhu_Singh_2020.JJMO01_contigs.tsv > vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_filt.vcf_unsort &
hash_into_vcf_id.pl -vcf variants.vcf -hash vigra.IA_panel.gwas.Sandhu_Singh_2020.JJMO01_contigs.tsv > vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_main.vcf_unsort &

# Add marker names in the third column. Names have the form:
#   1_1234  for markers on Vr01, position 1234
#  scaffold_567_9876   for markers on scaffold_567, position 9876
for file in *vcf_unsort; do
  perl -pi -e 's/^(\w+\.\w+\.\w+)\.(\w+)\t(\d+)\t\.\t/$1.$2\t$3\t$2_$3\t/; s/\tVr0(\d)/\t$1/; s/\tVr(\d+)/\t$1/' $file &
done


bcftools sort vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_filt.vcf_unsort > vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_filt.vcf &
bcftools sort vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_main.vcf_unsort > vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_main.vcf &

for file in vigra*vcf; do bgzip $file &
done

for file in vigra*vcf.gz; do tabix $file &
done



changes: 
  - 2021-09-16: Added full variants.vcf file, as vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_main.vcf.gz. 
                For both filtered and unfiltered vcf, added marker names, and changed contig/chrom names using 
                hash file vigra.VC1973A.gnm6.3nL8.scaff_name_hash.tsv, derived from GenBank JJMO01 contigs file.