bcftools VCFUtils error

Hi. I am running into a peculiar following error while trying to call the consensus fq file in the PSMC pipeline :

Use of uninitialized value $l in numeric lt (<) at /home/naman/soft/bcftools-1.10.2/bin/vcfutils.pl line 566, <> line 60613. Use of uninitialized value $l in numeric lt (<) at /home/naman/soft/bcftools-1.10.2/bin/vcfutils.pl line 566, <> line 60613.

I may be wrong that there is some issue with the input file. But I am not sure. This is the script I am following : $BCFTOOLS mpileup -C50 -f $REFERENCE input.bam | $BCFTOOLS call -c - | $VCFUTILS vcf2fq -d 10 -D 100 | gzip > output_diploid.fq.gz

Please note that I have processed over 40 samples with the same pipeline and script without any issues, but this is happening with 3 of the whole genome sequence. No issue with the RAW file, as the FastQC report looks good.

Thank you, and looking forward to understanding the issue.

Jun 18 '23 16:06 stachyris

Unfortunately, the vcfutils.pl script is no longer supported. I'll accept a pull request if anyone cares to fix it.

Just to cross link, this is a duplicate of #1811 and #1670

Jun 21 '23 12:06 pd3

Hi. Thanks for the response. I am wondering why this is working for some and why not for others. What could be the issue?

thank you, -Vinay

Jun 24 '23 08:06 stachyris