I can call snps but no indels through bcftools
1 2 3 4 5 6 7 8 9
ref: A A T T C C G G……
alt: A A A T T C C G G……
if my sequence act as above, then i use bcftools to call variance, it comes results as many snps in position 3, position 5, position 7……but no indels, however, actually it should be an indel (insert) at position 1 or 2.
I did the whole genome call variance, all results are snps but no indels, could anybody tell me how to solve this problem?
the commond line I used is as follows:
bcftools mpileup -Ou -f /annovar/db/a.fa /annovar/adb/C13.bam | \
bcftools call -Ou -mv | \
bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > C13.flt.vcf
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Bcftools consensus generates mismatched consensus sequence
written by Duy •
-
Consensus sequence calling with normalisation of indels
written by michael.flower.14 •
-
bcftools consensus
written by Giulia.cosenza •
-
Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )
written by Linda •
-
bcftools 1.4.1 call parameters
written by cetin.m
-
why I used bcftools mpilup and call commond, no indel variance were genearte?
written by lemon •
-
Indel calling from sanger reads
written by fabian.grammes •
-
Discrepancy between number of SNP calls using samtools/bcftools when --skip-indels flag used
written by TrentGenomics •
-
How to extract SNPs between samples and not between samples and reference
written by TrentGenomics •
-
Python - finding INDELS and SNPS
written by will.duncan26 •
Hello lemon!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!