-T option not working: "unknown file type"

[ElisabetThomsen]

Dear developers,

I am running hap.py on exome data. When I run hap.py with the -T option it gives error:

Exception: Command line bcftools view --threads 96 -O v /home/resources/GiaB/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz | bcftools view -O v -f PASS,. -T /home/resources/sureselect_human_all_exon_v6_utr_grch38/S07604624_Padded.bed | bcftools view -o /tmp/truth.pppzG_4f.vcf.gz -O z got return code 255.STDOUT: STDERR: [E::bcf_sr_regions_init] Could not parse the file /home/resources/sureselect_human_all_exon_v6_utr_grch38/S07604624_Padded.bed, using the columns 1,2[,-1]Failed to read the targets: /home/resources/sureselect_human_all_exon_v6_utr_grch38/S07604624_Padded.bedFailed to open -: unknown file type

When I run hap.py without the -T option it works with no error.

I am using hap.py 0.3.12 ( https://anaconda.org/bioconda/hap.py ) in a conda environment.

This is the command I used:

time hap.py /home/resources/GiaB/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz /home/run_exolink/phase/test_outs/phased_vcf/phased.vcf.gz -f /home//resources/GiaB/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed -o test_happy_out/NA12878test -r /home/resources/gatk_bundle/Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta -T /home/resources/sureselect_human_all_exon_v6_utr_grch38/S07604624_Padded.bed

Kind Regards
Elisabet

[ElisabetThomsen]

Hi,

I fixed this by modifying the BED file in this way:

awk 'BEGIN{OFS="\t"}{ if(NR <= 2) { print "#"$0 } else { print $1,$2,$3,$4,0,"." } }' S07604624_Padded.bed > S07604624_Padded_modified.bed

Commenting out the header lines and adding field 5 (with 0) and 6 (with ".").