Hi there! We sequenced some chicken genomic DNA (Illumina TruSeq, PE150), and I am trying to map the reads to reference genome with BWA mem and then call SNPs with GATK. I used the default settings of BWA, and checked the alignment statistics by using samtools flagstat. I got a 99% mapping rate. Does this mapping rate seem to be in normal range? I'm very new to DNA-seq alignment. It would be great if you guys could give me some suggestions about adjusting BWA parameters for PE150. Any input will be appreciated!
•
written
by
zhuozhu132 •
1 answer
I don't see any reason why you shouldn't see this kind of alignment rate at all. We would expect to achieve this with our mammalian sequencing projects.
I'm sure the default settings for bwa mem are fine for your application.
I'd suggest FreeBayes for your genotyping - it will probably save you some time and effort over GATK.
Log in to answer this question.
-
Alignment report
written by shivangi.agarwal800
-
Alignment using BWA tool
written by kriti.awasthi23 •
-
Low mapping rate for human NGS PE reads to hs37d5 genome
written by Ginsea Chen
-
Pindel lower the mutation rate in indel calling
written by jinxinhao1988
-
bwa mem -T (alignment score) not doing anything
written by chris.bird •
-
Suggest an alignment tool for MinION reads
written by vkgaur25 •
-
How to compare coverage eveness of two whole genome sequencing runs of the same sample?
written by xuang •
-
RNA-seq read alignment
written by amy16 •
-
Weird alignments in amplicon sequencing
written by kulvait
-
BWA MEM and ancient DNA
written by smilefreak
