Input not detected as vcf or bcf format

[cantlap]

Getting this error:

[E::bcf_hdr_read] Input is not detected as bcf or vcf format bcftools: bgzf.c:982: bgzf_read: Assertion `fp->is_write == 0' failed. Failed to open -: unknown file type index: "-" is in a format that cannot be usefully indexed

When I try to run this script file:

bpm_manifest_file="/home/cantlap/illumina_gtc_conversion/gsa2022_redo/GSA_Product_Files/GSA-24v3-0_A2.bpm" csv_manifest_file="/home/cantlap/illumina_gtc_conversion/gsa2022_redo/GSA_Product_Files/GSA-24v3-0_A2.csv" egt_cluster_file="/home/cantlap/illumina_gtc_conversion/gsa2022_redo/GSA_Product_Files/GSA-24v3-0_A1_ClusterFile.egt" path_to_gtc_folder="/home/cantlap/illumina_gtc_conversion/gsa2022_redo/gtcList_gsa2022_redo.txt" ref="/home/cantlap/illumina_gtc_conversion/gsa2022_redo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna" out_prefix="/home/cantlap/illumina_gtc_conversion/gsa2022_redo/outputVCF_files" bcftools +gtc2vcf \ --no-version -Ou \ --bpm $bpm_manifest_file \ --csv $csv_manifest_file \ --egt $egt_cluster_file \ --gtc-list $path_to_gtc_folder \ --fasta-ref $ref \ --output $out_prefix.tsv | \ bcftools sort -Ou -T ./bcftools. | \ bcftools norm --no-version -Ob -c x -f $ref | \ tee $out_prefix.bcf | \ bcftools index --force --output $out_prefix.bcf.csi

[freeseek]

When you use --output the bcftools +gtc2vcf plugin will not pipe anything to stdout for the bcftools sort command to read

[cantlap]

When I run with the --extra tag which is what is listed on the instructions it gives this error though:

bash runGTC2VCF.sh Writing to ./bcftools. gtc2vcf: unrecognized option '--extra'

About: convert Illumina GTC files containing intensity data into VCF (2018-09-07)

Usage: bcftools +gtc2vcf [options] <A.gtc> [...]

[freeseek]

You are using an extremely old versin of bcftools +gtc2vcf that does not have that option