Input not detected as vcf or bcf format
cantlap opened this issue · comments
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
When you use --output the bcftools +gtc2vcf plugin will not pipe anything to stdout for the bcftools sort command to read
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> [...]
You are using an extremely old versin of bcftools +gtc2vcf that does not have that option