Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
PacBio consensus quality phleroy Pacific Biosciences 6 02-12-2019 09:22 AM
Consensus Calling BCFTOOLS PacBio gaps uloeber Bioinformatics 2 07-27-2017 03:18 AM
Tools to generate VCF from two FASTA, or mutant FASTA from Ref FASTA and VCF? jeffseq Bioinformatics 3 05-28-2013 11:59 AM
New consensus from VCF dbrami Bioinformatics 9 09-20-2012 11:35 PM

Thread Tools
Old 10-29-2020, 04:58 PM   #1
Location: Raleigh, NC

Join Date: Nov 2008
Posts: 51
Default PacBio software vcf and consensus fasta do not agree

I'm using PacBio's "variantCaller" tool (v6) to call variants on some older RSII subread data I aligned with blasr. The reference is 14845 bp.

My variantCaller command is:

variantCaller --algorithm arrow --log-file variantCaller.log --annotateGFF --reportEffectiveCoverage --noEvidenceConsensusCall lowercasereference --minCoverage 40 --coverage 100 --minMapQV 40 --minConfidence 10 --minReadScore 0.75 --minSnr 3.75 --minZScore -3.5 --minAccuracy 0.82  --numWorkers 5 -r ref.fa -o 129C02-vs-ref.fa.sort.vcf -o 129C02-vs-ref.fa.sort.gff -o 129C02-vs-ref.fa.sort.fasta -o 129C02-vs-ref.fa.sort.fastq 129C02-vs-ref.fa.sort.bam
Now it is my understanding that the fasta (and fastq) output this command should reflect the differences between the reference and the reads as reported in the vcf output.

My vcf file reports:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
ref    11438   .       CA      C       25      PASS    DP=100
However when I align the reference and this fasta output 2 1-bp deletions are observed. One is the deletion in the vcf. The other is several thousand base pairs away and is not called by variantCaller.

This, of course, is very disturbing. Can you explain this?

Thanks for your help
Mark is offline   Reply With Quote

consensus, pacbio, variant, variantcaller, vcf

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:33 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO