Hello,
I am trying to find indels using Bowtie2 and samtools from some illumina runs of a few bacterial genomes.
The sequenced samples are from a directed evolution study, so I would expect the SNPs and indels from the starting sample to be propagated through.
In about 4 of the 16 sequenced samples, I have a indel called at one location (including the starting sample), but the others call this as a SNP. If I look at the vcf file, I see that it is using only a small fractions of the reads to call the SNP (ie, DP=200-400 and the sum of the high quality reads DP4 ~ 20-40). Also, in tablet it looks like there should be an indel there.
Has anyone run into the problem where samtools discards many of the reads due to "low quality"?
Side notes: I've actually recently started to use the IndelRealigner from GATK and can get these locations to be called as indels, but still many of the reads are not being used.
I should also mention that one half of the samples (those that had some problems) were with the phred64+ and not the phred33.
Thanks for your help!
I am trying to find indels using Bowtie2 and samtools from some illumina runs of a few bacterial genomes.
The sequenced samples are from a directed evolution study, so I would expect the SNPs and indels from the starting sample to be propagated through.
In about 4 of the 16 sequenced samples, I have a indel called at one location (including the starting sample), but the others call this as a SNP. If I look at the vcf file, I see that it is using only a small fractions of the reads to call the SNP (ie, DP=200-400 and the sum of the high quality reads DP4 ~ 20-40). Also, in tablet it looks like there should be an indel there.
Has anyone run into the problem where samtools discards many of the reads due to "low quality"?
Side notes: I've actually recently started to use the IndelRealigner from GATK and can get these locations to be called as indels, but still many of the reads are not being used.
I should also mention that one half of the samples (those that had some problems) were with the phred64+ and not the phred33.
Thanks for your help!
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