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This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
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[E::bcf_get_variant_type] Requested allele outside valid range #2086

Closed MartaAlberti closed 5 months ago

MartaAlberti commented 6 months ago

Hello, I am trying to generate some basic statistics about VCFs, to do so I used: bcftools stats hgdp_wgs.20190516.full.chr22.vcf.gz which works fine. However when I try to generate stats about the samples with the command: bcftools stats -s - hgdp_wgs.20190516.full.chr22.vcf.gz I get the following error:

[E::bcf_get_variant_type] Requested allele outside valid range

bcftools_error

I am using raw HGDP VCFs which I downloaded with; wget ftp://ngs.sanger.ac.uk/production/hgdp/hgdp_wgs.20190516/hgdp_wgs.20190516.full.chr*.vcf.gz

and I get the same error with all the chromosomes, so not only with chr22.

What causes this error and what can I do to solve it?

Thank you!!

Marta

ghuls commented 5 months ago

It chokes on line 3517:

$ zcat hgdp_wgs.20190516.full.chr22.vcf.gz | head -n 3517 |tail -n 1 | tr '\t' '\n'
chr22
10516102
rs1165478523
ATG
GTG,A
3408.15
PASS
AC=6,5;AF=0.0121951,0.0101626;AN=492;BaseQRankSum=0.89;ClippingRankSum=-0.702;DP=7557;ExcessHet=0;FS=6.613;InbreedingCoeff=0.2523;MLEAC=13,7;MLEAF=0.00963,0.005185;MQ=4.2;MQRankSum=0.373;QD=20.05;ReadPosRankSum=0.421;SOR=0.474;VQSLOD=-0.002;culprit=FS;VQSRMODE=INDEL;NS=246;ExcHet=0,0
GT:AD:DP:GQ:PGT:PID:PL
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./.:8,0,0,0:8:12:.:.:0,12,180,12,180,180
0/0:19,0,0,0:19:48:.:.:0,48,720,48,720,720
./.:0,1,1,1:1:.:.:.:.
./.:2,0,0,0:2:.:.:.:.
0/0:35,0,0,0:35:90:.:.:0,90,1350,90,1350,1350
2/2:0,0,10,0:10:30:.:.:446,447,447,30,30,0
0/0:18,0,0,0:18:51:.:.:0,51,765,51,765,765
./.:1,0,0,0:1:3:.:.:0,3,42,3,42,42
./.:13,3,3,3:16:0:.:.:0,0,440,0,440,440
0/1:4,4,0,0:8:99:.:.:116,0,117,128,129,257
./.:2,2,2,2:4:0:.:.:0,0,5,0,5,5
./.:3,0,0,0:3:3:.:.:0,3,45,3,45,45
0/0:27,1,1,1:28:60:.:.:0,60,1058,60,1058,1058
./.:5,0,0,0:5:6:.:.:0,6,90,6,90,90
./.:0,0,0,0:0:.:.:.:.
./.:7,0,0,0:7:6:.:.:0,6,90,6,90,90
./.:2,0,0,0:2:3:.:.:0,3,45,3,45,45
./.:11,1,1,1:12:0:.:.:0,0,412,0,412,412
0/0:15,0,0,0:15:42:.:.:0,42,630,42,630,630
./.:3,0,0,0:3:6:.:.:0,6,90,6,90,90
./.:4,0,0,0:4:6:.:.:0,6,90,6,90,90
0/1:13,4,0,0:17:93:.:.:93,0,443,133,455,587
./.:1,0,0,0:1:3:.:.:0,3,42,3,42,42
./.:4,3,3,3:7:0:.:.:0,0,43,0,43,43
./.:3,1,1,1:4:0:.:.:0,0,74,0,74,74
./.:1,2,2,2:3:.:.:.:.
./.:0,2,0,0:2:6:.:.:68,6,0,68,6,68
pd3 commented 5 months ago

When GT is missing but AD is present, the program determines the alternate allele from AD. However, if the AD tag has incorrect number of values, the program would exit with an error printing "Requested allele outside valid range". This is now fixed by taking into account the actual number of ALT alleles.

Thank you for the bug report.