Chimeric reads in Samtools depth & fastq
Chimeric reads
Reads are splited and aligned to reference genome separately.
Samtools flag 2048
1 | samtools view -F 2048 |
can easliy exclude chimeric reads
Different strategies in Samtools fastq & depth
1 | samtools fastq |
does not include any chimeric reads in output file
1 | samtools depth |
However, count all reads including chimeric
**Warning: Output from samtools fastq and samtools depth can be inconsistent **