Greetings, Do you still support vcfutils for the purposes of this pipeline 'samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq'?
I have been trying to generate some short 25mer fastq sequences and so far it has worked fine, with two exceptions. Firstly, I did have to modify the code at line 521 (I think) just to get it to write a proper fq. Second issue is this error: substr outside of string at /usr/local/bin/vcfutils.pl line 557, <> line 141. Use of uninitialized value in lc at /usr/local/bin/vcfutils.pl line 557, <> line 141. substr outside of string at /usr/local/bin/vcfutils.pl line 557, <> line 141. So far I have only seen this in one vcf. Samples below #CHROM POS ID REF ALT 6 36853784 . C . 6 36853785 . G . 6 36853786 . A . 6 36853786 . AGGGG AGGGGG 6 36853787 . G . 6 36853787 . G . 6 36853788 . G . 6 36853789 . G . 6 36853790 . G . 6 36853790 . GC G 6 36853791 . C . 6 36853792 . G . 6 36853793 . C . 6 36853794 . G . 6 36853795 . A . 6 36853796 . G . 6 36853797 . C . 6 36853798 . C . 6 36853799 . C . 6 36853800 . C . 6 36853801 . G . 6 36853802 . C . 6 36853803 . A . 6 36853804 . T . 6 36853805 . G . 6 36853806 . T . Any insight into what might be happening? I have I have been clear and provided relevant information. Please let me know. Thank you. -bwubb ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
