VCF input not working

[marchoeppner]

Hi,

so I have variant calls (vcf.gz) for chrY (hg38) - and was hoping to get a haplogroup inference like so:

Yleaf -vcf Y.vcf.gz -rg hg38 -o results

Sadly, the resulting inference is:

Sample_name     Hg      Hg_marker       Total_reads     Valid_markers   QC-score        QC-1    QC-2    QC-3
Y.filtered      NA              VCF     380     NA      NA      NA      NA

The log reports no errors, so I am unsure what the issue is here.

DEBUG 10:16:59.246446 (0.000 s) - Logger created
INFO 10:16:59.246523 (0.000 s) - Running Yleaf with command: /home/marc/.local/bin/Yleaf -vcf Y.vcf.gz -rg hg38 -o results
DEBUG 10:16:59.263808 (0.018 s) - Started running the following command: bcftools sort -O z -o results/Y.sorted.vcf.gz Y.vcf.gz
DEBUG 10:16:59.404143 (0.158 s) - Finished running the command bcftools sort -O z -o results/Y.sorted.vcf.gz Y.vcf.gz
DEBUG 10:16:59.404270 (0.158 s) - Started running the following command: bcftools index -f results/Y.sorted.vcf.gz
DEBUG 10:16:59.429212 (0.183 s) - Finished running the command bcftools index -f results/Y.sorted.vcf.gz
DEBUG 10:16:59.486384 (0.240 s) - Started running the following command: bcftools view -O z -R results/Ytemp_position_bed.bed results/Y.sorted.vcf.gz > results/filtered_vcf_files/Y.filtered.vcf.gz
DEBUG 10:17:02.844021 (3.598 s) - Finished running the command bcftools view -O z -R results/Ytemp_position_bed.bed results/Y.sorted.vcf.gz > results/filtered_vcf_files/Y.filtered.vcf.gz
DEBUG 10:17:02.844134 (3.598 s) - Started running the following command: rm results/Ytemp_position_bed.bed
DEBUG 10:17:02.850847 (3.605 s) - Finished running the command rm results/Ytemp_position_bed.bed
DEBUG 10:17:02.850945 (3.605 s) - Started running the following command: rm results/Y.sorted.vcf.gz
DEBUG 10:17:02.854960 (3.609 s) - Finished running the command rm results/Y.sorted.vcf.gz
DEBUG 10:17:02.855059 (3.609 s) - Started running the following command: rm results/Y.sorted.vcf.gz.csi
DEBUG 10:17:02.858930 (3.613 s) - Finished running the command rm results/Y.sorted.vcf.gz.csi
DEBUG 10:17:02.975893 (3.730 s) - Starting with extracting haplogroups...
DEBUG 10:17:03.076025 (3.830 s) - Started running the following command: bcftools query -f '%CHROM      %POS    %REF    %ALT[   %AD]
' results/filtered_vcf_files/Y.filtered.vcf.gz > results/Y.filtered/Y.filtered.txt
DEBUG 10:17:03.092079 (3.846 s) - Finished running the command bcftools query -f '%CHROM        %POS    %REF    %ALT[   %AD]
' results/filtered_vcf_files/Y.filtered.vcf.gz > results/Y.filtered/Y.filtered.txt
DEBUG 10:17:03.095061 (3.849 s) - Started running the following command: rm results/Y.filtered/Y.filtered.txt
DEBUG 10:17:03.099561 (3.853 s) - Finished running the command rm results/Y.filtered/Y.filtered.txt
INFO 10:17:03.219902 (3.974 s) - Finished extracting genotypes for Y.filtered.vcf.gz
INFO 10:17:03.286277 (4.040 s) - Starting haplogroup prediction...
DEBUG 10:17:03.392698 (4.146 s) - Finished haplogroup prediction
INFO 10:17:03.392918 (4.147 s) - Done!

Yleaf version is 3.2.1.