Hi,
I am new with REViewer can I encounter an error with the "BGZF header".
As output i get an empty ".metrics.tsv" and ".phasing.tsv" file and no images.
Do you know a solution for this?
BAM_EXPANSIONHUNTER="patientID_realigned.bam"
samtools sort patientID_realigned.bam -o patientID_realigned.sorted.bam
samtools index patientID_realigned.sorted.bam patientID_realigned.bam.bai
$ REViewer \
--reads $BAM_EXPANSIONHUNTER \
--vcf $VCF_EXPANSIONHUNTER \
--reference $REFERENCE_GENOME \
--catalog $VARIANT_CATALOG \
--locus AFF2,AR,ATN1,ATXN1,ATXN10,ATXN2,ATXN3,ATXN7,ATXN7,ATXN8OS,ATXN8OS,C9ORF72,CACNA1A,CBL,CNBP,CSTB,DIP2B,DMPK,FMR1,FXN,GIPC1,GLS,HTT,JPH3,NIPA1,NOP56,NOTCH2NL,PABPN1,PHOX2B,PPP2R2B,RFC1,TBP,TCF4 \
--output-prefix $OUTPUT_PREFIX
[2022-10-28 13:21:13.966] [info] Loading specification of locus AFF2
[E::bgzf_read_block] Invalid BGZF header at offset 590043
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[2022-10-28 13:21:13.968] [info] Extracted 0 frags
[2022-10-28 13:21:13.968] [info] Calculating fragment length
[2022-10-28 13:21:13.974] [error] There are no read alignments in the target region
Hi, I am new with REViewer can I encounter an error with the "BGZF header". As output i get an empty ".metrics.tsv" and ".phasing.tsv" file and no images. Do you know a solution for this?
BAM_EXPANSIONHUNTER="patientID_realigned.bam" samtools sort patientID_realigned.bam -o patientID_realigned.sorted.bam samtools index patientID_realigned.sorted.bam patientID_realigned.bam.bai
$ REViewer \
I appreciate your help, /Tine