Hi !
I am trying to use freeBayes for variant calling and run into problems with the example provided in the freeBayes package.
When I run the following pipeline given in the package, I get the warnings stated below for most of the reads in my bamfiles
#!/bin/bash
outdir=OUTPUT
mkdir -p $outdir
reference=REFERENCE.fasta
bamlist=BAMFILENAMES.txt
cnvmap=CNVMAP.bed
region=REGION
time /share/home/erik/bin/bamtools merge -region $region \
$(for file in $(cat $bamlist); do echo " -in "$file; done) \
| time /share/home/erik/bin/ogap -z -R 25 -C 20 -Q 20 -S 0 -f $reference \
| time /share/home/erik/bin/bamleftalign -f $reference \
| time /share/home/erik/bin/samtools calmd -EAru - $reference 2>/dev/null \
| time /share/home/erik/bin/freebayes \
--min-alternate-count 2 \
--min-alternate-qsum 40 \
--pvar 0.0001 \
--use-mapping-quality \
--posterior-integration-limits 1,3 \
--genotype-variant-threshold 4 \
--site-selection-max-iterations 3 \
--genotyping-max-iterations 25 \
--max-complex-gap 3 \
--cnv-map $cnvmap \
--stdin \
--region $region \
-f $reference \
| gzip >$outdir/$region.vcf.gz
the output consists of many warnings (exceptions, basically for every read in my bamfiles) of the form
exception when realigning HWI-D00432:140126:C3KE2ACXX:1:2301:14872:89688 at position chr1:236849712 GTCCGCCCGCACGTGCTCGGGGCGGGGCGGCTGGGGCCCGACGGGCGGGGCCGGGGGCGGTGGCGGCGGGGGCGTGGCCGGGCGGCCACGTGACGGGCGGCGCGGCTATTAAGCCGCGCGG CCGGGGGCGGTGGCGGCGGGGG
CGCACGTGCTCGGGGCGGGGCGGCTGGGGCCCGACGGGCGGGGCCGGGGGCGGTGGCGGCGGGGGCGTGGCCGGGCGGCCACGTGACGGGCGGCGCGGCTATTAAGCCGCGCGGCAGCTGCTCGCAGCCGGAGCTGGTGCTT
CGGTGGCGGCGGGGGCGTGGCCGGGCGGCCACGTGACGGGCGG
I could not figure out why this happens and how to solve the problem.
It seems that the message is generated by ogap.cpp .
Any help is appreciated.
Thanks!
I am trying to use freeBayes for variant calling and run into problems with the example provided in the freeBayes package.
When I run the following pipeline given in the package, I get the warnings stated below for most of the reads in my bamfiles
#!/bin/bash
outdir=OUTPUT
mkdir -p $outdir
reference=REFERENCE.fasta
bamlist=BAMFILENAMES.txt
cnvmap=CNVMAP.bed
region=REGION
time /share/home/erik/bin/bamtools merge -region $region \
$(for file in $(cat $bamlist); do echo " -in "$file; done) \
| time /share/home/erik/bin/ogap -z -R 25 -C 20 -Q 20 -S 0 -f $reference \
| time /share/home/erik/bin/bamleftalign -f $reference \
| time /share/home/erik/bin/samtools calmd -EAru - $reference 2>/dev/null \
| time /share/home/erik/bin/freebayes \
--min-alternate-count 2 \
--min-alternate-qsum 40 \
--pvar 0.0001 \
--use-mapping-quality \
--posterior-integration-limits 1,3 \
--genotype-variant-threshold 4 \
--site-selection-max-iterations 3 \
--genotyping-max-iterations 25 \
--max-complex-gap 3 \
--cnv-map $cnvmap \
--stdin \
--region $region \
-f $reference \
| gzip >$outdir/$region.vcf.gz
the output consists of many warnings (exceptions, basically for every read in my bamfiles) of the form
exception when realigning HWI-D00432:140126:C3KE2ACXX:1:2301:14872:89688 at position chr1:236849712 GTCCGCCCGCACGTGCTCGGGGCGGGGCGGCTGGGGCCCGACGGGCGGGGCCGGGGGCGGTGGCGGCGGGGGCGTGGCCGGGCGGCCACGTGACGGGCGGCGCGGCTATTAAGCCGCGCGG CCGGGGGCGGTGGCGGCGGGGG
CGCACGTGCTCGGGGCGGGGCGGCTGGGGCCCGACGGGCGGGGCCGGGGGCGGTGGCGGCGGGGGCGTGGCCGGGCGGCCACGTGACGGGCGGCGCGGCTATTAAGCCGCGCGGCAGCTGCTCGCAGCCGGAGCTGGTGCTT
CGGTGGCGGCGGGGGCGTGGCCGGGCGGCCACGTGACGGGCGG
I could not figure out why this happens and how to solve the problem.
It seems that the message is generated by ogap.cpp .
Any help is appreciated.
Thanks!
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