sam2cov

This C program creates coverage files for sam files. The sam format is specified here, while the output is in BED format .

Usage

    Usage: sam2cov [OPTIONS] fai_file sam_file
    Options:
        -r  Aligned with RUM? [0/1] Default: 0
        -s  Strand: 1 for fwd, 2 for rev [0/1/2]. Default: 0
            Please note: Reads are assumed to be in Illumina R2-R1 orientation!
        -e  Paired end mode [0/1] Default: 1
        -p  Prefix for coverage files. Default: Unique.cov, NU.cov
        -u  Print header for UCSC Genome browser? [0/1] Default: 0
        -h  This helpful message.
        -v  Print Version.

Example

• For a sam file produced by STAR or GSNAP:

  sam2cov -p coverage_ danRer7.fa.fai test.sam

• For a sam file produced by RUM:

  sam2cov -p coverage_ -r 1 danRer7.fa.fai test.sam

Note: To create the fa.fai use samtools faidx danRer7.fa. Samtools can be downloaded here.

Installation

git clone https://github.com/khayer/sam2cov.git
cd sam2cov
make

Requirements

• You will need at least 15G of RAM, depending on the size of the genome.
• You will also need 'cc'.

Limitations

• Reads in sam file can't be longer than 5,000 characters.
• Sam files produced by other aligners than STAR, GSNAP and RUM are currently not supported.
• Sam files have to be sorted by sequence name.
• Read pairs can't be separated. This is especially important for multi-mappers.

troubleshoot

• Add -std=gnu99 to the makefile if you see this bug:

sam2cov.c:103: warning: implicit declaration of function ‘getopt’