Jean Peccoud

samtools commands should use the bam index to speed up operations

4

#### Is your feature request related to a problem? Please specify. The samtools commands that take a bed file as argument to work on selected genomic regions or positions ,...

mpileup read-pair overlap detection not detecting all overlaps?

18

Checked on both samtools 1.9 on macOS and samtools 1.5 on Redhat Linux Steps: Decompress and index the attached bam file with `samtools index AV-WXa1591_m_scaffold1.bam` then `samtools mpileup -A -Q1...

What settings should I choose.

1

Hello, I have tested this tool to assemble a genome on sequel II data (ccs), but I have no idea what setting I should tweak to improve the results. The...