Problem detecting indels
I´m working with a list of consensus sequences in order to detect variants. I´ve map the consensus to the references senquence using Needleall or BWA-MEM and calling variants with freebayes (v0.9.21). When I check SAM file I can detect indels, but in the vcf generated by freebayes, only SNPs are reported.
Example: AACACACAACAAGAA 0 HXB2_reference 1 255 2D211M1D2M4D9M3I3M2I240M
Could you help me, please?
• 2,028 views
•
link
updated
by
gb
•
written
by
Estrella •
•
written
by
Estrella •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
alignement and Variant calling with BWA and samtools
written by simon.burgermeister •
-
How to get cigar string from bwa or bowtie
written by juan.crescente •
-
DNAseq pipeline steps
written by shuksi1984 •
-
Is there something wrong with my Indel Calling protocol?
written by lishen0709 •
-
Extract soft-clipped reads from BWA -generated SAM file
written by ThePresident
-
calling variants between two strains
written by steven.lin.pur •
-
Lack of consensus between NGS & Sanger sequencing on indels/mutations
written by alons
-
BWA Small Indels vs Roche Newbler Assembler
written by pld
-
Which Reference Index to use for Clinical Variants (SNPs and INDELs) Detection ?
written by cvu
-
Paired-End Reads Alignment For Variant Calling ?
written by newDNASeqer
just because you found one read with a deletion doesn't mean that a variant will be generated. Now, it doesn't explain why there is not any indel withh freebayes.
Thank you Pierre. I agree. But, for example, in position 2 IGV detects 140 deletions (total consensus sequences: 56452). I´ve tested with the freebayes naive option, without better results :S
What is your freebayes command? Did you checked the default values.
-Fcould be a startHi gb, Everytime I try with -F 0 , I obtain something similar to:
HXB2_reference 2 . GGAATTTTC GTACTTGTC,GTACTTGGC,TGTCTTTTC,TGACTTGTC,TGACTTGGC,TGACTTTGC,TGACTTTTC,TGAAGTTTC,TGAATTGTC,TGAATTGGC,TGAATTTGC,GGCAGTGGC,TTACTTGTC,CTACTTTTC,TTACTTTTC,GGACTTCTC,GGACTTGTC,GGACTTGGC,GGACTTTGC,GC,GGC,TTAATTTTC,GTAATTTTC,AGAATTTTC,TGAATTTTC,GGCATTTTC,GGGATTTTC,GGTATTTTC,GGACTTTTC,GGAATTATC,GGAATTCTC,GGAATTGTC,GGAATTTCC,GGAATTTGC,GGAATTTTA
(and no more variants)
The default value for F is 0.2, and, if I am rigth, it suppose that, in a certain position, if I have > 13 deletions (for a total of 56452 consensus sequences), it might be shown, isn´t it?
In the same way, I´ve tried with -C 1, with and without -F 0. In the first option, I obtain a list of variants, but any of them is a indel.
One question: if in a position freebayes detect SNP and indels, it can return both of them?
Thank you so much
No? 0.2=20% 13 of 56452 is like 0.02%
Yes
You can also check out vcfallelicprimitives https://github.com/vcflib/vcflib/blob/master/doc/vcfallelicprimitives.md
Mostly for variantcalling you map reads instead of consensus sequences so not sure if that has an influence on the algoritm.