Failed conversion <int>
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Hello,
I have a vcf of haplotypoes produced by Shapeit2. When trying to convert, GEVA throws an uninformative error:
Error: Failed conversion in field 0, token: chr10
Do you have an example of a VCF file that works, please?
The header and the first few lines of mine:
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=31032021_20h19m15s
##source=SHAPEIT2.v837
##log_file=shapeit_31032021_20h19m15s_1cb2981d-f0ec-4662-903d-2ac19badbf2b.log
##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
##contig=<ID=chr10>
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view -R Herato_final.chr10.mask.bed.gz -Oz -o chr10.phased.masked.vcf.gz chr10.shapeit_phased.vcf.gz; Date=Tue Jul 27 10:57:42 2021
##bcftools_viewCommand=view -t chr10:4600000-4760000 -Oz -o wnta.phased.erato.vcf.gz chr10.phased.masked.vcf.gz; Date=Tue Jul 27 11:24:01 2021
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT amalfredaBC2115 amalfredaBC2124 amalfredaPF268 amalfredaPF269 amalfredaPF320 amalfredaPF322 amalfredaSR214 amalfredaSTRI5779 amalfredaSTRI5780 amalfredaSTRI5781 amazonaKK165 amazonaKK166 amazonaKK168 amazonaKK181 amazonaKK189 amazonaKK190 amazonaKK214 amazonaKK216 amazonaKK217 amazonaKK225 amazonaSR1 amazonaSR122 amazonaSR125 amazonaSR126 amazonaSR127 amazonaSR71 amazonaSR72 amazonaSR73 amazonaSR79 amazonaSR80 amphitriteKK462 amphitriteKK463 amphitriteKK464 amphitriteKK491 amphitriteKK492 amphitriteKK497 amphitriteKK520 amphitriteKK522 amphitriteKK528 chestertonii0057 chestertonii0058 chestertonii0059 chestertonii3661 chestertonii3662 chestertonii3663 chestertonii3664 colombinaM4164 cruentusMRKMX0901 cyrbia004 cyrbia005 cyrbia023 cyrbia024 demophoonCAM2980 demophoonCAM2981 demophoonCAM618 demophoonSTRI1284 demophoonSTRI33 demophoonSTRI5353 demophoonSTRI5632 demophoonSTRI87 dignusCAM40106 dignusCAM40111 dignusCAM40112 dignusCAM40113 dignusCAM40114 emmaGS020 emmaGS021 emmaKK401 emmaKK402 emmaKK403 emmaKK595 emmaKK599 emmaNCS1671 emmaNCS1672 emmaNCS1673 emmaNCS1674 emmaNCS1675 eratoNCS2005 eratoNCS2012 eratoNCS2020 eratoNCS2023 eratoNCS2025 eratoNCS2556 estrella16HE037 estrella16HE043 etylusBC3277 etylusBC3278 etylusBC3280 etylusBC3281 etylusBC3282 etylusCAM9128 favorinusGS012 favorinusNCS0471 favorinusNCS0473 favorinusNCS0476 favorinusNCS0478 favorinusNCS0479 favorinusNCS2554 favorinusNCS2555 guaricaM3121 guaricaM3125 guaricaM3375 guaricaM3376 guaricaM3428 hydaraHE1 hydaraHE2 hydaraNCS1179 hydaraNCS1979 hydaraNCS2080 hydaraNCS2211 hydaraNCS2217 hydaraNCS2581 hydaraNCS2609 hydaraSTRI354 hydaraSTRI359 hydaraSTRI39 hydaraSTRI40 hydaraSTRI42 hydaraSTRI5193 hydaraSTRI5351 hydaraSTRI88 hydaraxamalfredaSR165 hydaraxamalfredaSR166 hydaraxamalfredaSR198 hydaraxamalfredaSR200 lativitta02 lativitta03 lativitta04 lativittaBC0411 lativittaCAM40133 lativittaCAM40139 lativittaCAM40158 lativittaCAM40160 lativittaCAM40162 lativittaM3747 lativittaM4457 lativittaM4458 lativittaM4461 luscombeiKK580 luscombeiSTRI5771 luscombeiSTRI5772 microcleaKK333 microcleaKK334 microcleaKK338 notabilis01 notabilis02 notabilis03 notabilis04 notabilisBC0410 notabilisBC3066 notabilisBC3223 notabilisBC3224 notabilisBC3225 notabilisBC3227 notabilisBC3228 petiveranaCA51 petiveranaCA53 petiveranaCA54 petiveranaCA55 petiveranaCA56 petiveranaED3 petiveranaKK722 petiveranaSTRI2936 petiveranaSTRI2942 petiveranaSTRI2943 petiveranaSTRI2944 petiveranaSTRI2945 phyllis16HE051 phyllis16HE052 phyllis16HE087 phyllis16HE088 phyllis16HE094 phyllisKK101 phyllisKK102 phyllisKK103 phyllisKK104 phyllisKK105 phyllisSR230 phyllisSR232 phyllisSR233 phyllisSR258 phyllisSR284 phyllisSR285 phyllisSR300 phyllisSR385 phyllisSR389 phyllisSTRI5732 phyllisSTRI5742 phyllisSTRI5765 phyllisSTRI5766 reductimaculaCAR291 reductimaculaCAR297 reductimaculaCAR298 reductimaculaM4050 reductimaculaM4051 reductimaculaM4053 reductimaculaM4054 reductimaculaM4055 reductimaculaTUP317 venusM3654 venusM3655 venusM3656 venusM3657 venusM3659 venustusSR309 venustusSR314 venustusSR334 venustusSR344 venustusSR354
chr10 4600139 . T A . PASS . GT 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|0 1|1 1|0 1|1 1|0 0|0 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 0|0 1|1 1|0 1|1 1|1 1|0 1|1 1|0 1|1 1|1 1|0 1|0 1|0 0|1 0|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 0|1 1|1 0|1 1|0 0|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1
chr10 4600141 . T C . PASS . GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
chr10 4600144 . A C . PASS . GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
chr10 4600232 . A G . PASS . GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 1|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1|0 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 1|1 0|1 1|1 1|0 1|1 0|0 1|1 1|1 1|1 1|1 0|1 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|1
Huh, it expects the chromosome names to be integers (even though the example of a map in the manual has a chromosome named "chr1"). Caveat emptor!