Hi,
I call bwa using default parameters except that I use -s parameter to “disable Smith-Waterman for the unmapped mate” for bwa sampe.
For output bam file, I find that there are many reads alignments with more than one gaps, with cigar string such as 4M1I2M1D17M1I50M.
According to my understanding, bwa aln uses -o parameter to control the maximum number of gap opens and the default value is 1.
Why are there so many output alignments with more than one gaps?
My bwa version is 0.6.1-r104 and use bwa as follows
bwa aln first_reads.fastq >first_reads.sai
bwa aln second_reads.fastq >second_reads.sai
bwa sampe -s first_reads.sai second_reads.sai first_reads.fastq second_reads.fastq |samtools view -bS /dev/stdin >output.bam
thanks
I call bwa using default parameters except that I use -s parameter to “disable Smith-Waterman for the unmapped mate” for bwa sampe.
For output bam file, I find that there are many reads alignments with more than one gaps, with cigar string such as 4M1I2M1D17M1I50M.
According to my understanding, bwa aln uses -o parameter to control the maximum number of gap opens and the default value is 1.
Why are there so many output alignments with more than one gaps?
My bwa version is 0.6.1-r104 and use bwa as follows
bwa aln first_reads.fastq >first_reads.sai
bwa aln second_reads.fastq >second_reads.sai
bwa sampe -s first_reads.sai second_reads.sai first_reads.fastq second_reads.fastq |samtools view -bS /dev/stdin >output.bam
thanks