Support GATK 4

[vladsavelyev]

Hi,

Thank you for an awesome tool. Great that have a replacement for Contest and VerifyBAMID.

My question is whether you had a chance to test it with GATK 4. GATK4 has a different command line interface, in particular -T Pileup goes into just Pileup, -o translates into capital -O, and read filter flags are a bit renamed and set with -RF. So the Pileup calling code could look like the following:

if gatk_type == "gatk4":
    command_line = ("{7} {0} -Xmx{1} -jar {2} Pileup -R {3} -I {4} -L {5} -O {6} " +
                    "-verbose -RF NotDuplicateReadFilter -RF CigarContainsNoNOperator " +
                    "-RF MatchingBasesAndQualsReadFilter").format(JAVA_TEMP, opts.xmx_java, GATK, REFERENCE, opts.bam, MARKER_FILE, opts.outfile, opts.java)
else:
    command_line = ("{7} {0} -Xmx{1} -jar {2} -T Pileup -R {3} -I {4} -L {5} -o {6} " +
                    "-verbose -rf DuplicateRead --filter_reads_with_N_cigar " +
                    "--filter_mismatching_base_and_quals").format(JAVA_TEMP, opts.xmx_java, GATK, REFERENCE, opts.bam, MARKER_FILE, opts.outfile, opts.java)

Since GATK4 is open source and available on bioconda, it would make it easier to distribute Conpair with bioconda as well, and further add it into frameworks like bcbio-nextgen.

For the sake of bioconda, it would be convenient to additionally support the gatk executable wrapper when it's in PATH. So instead of calling:

java -Xmx12g -jar gatk4-4.0.7.0-0/gatk-package-4.0.7.0-local.jar Pileup 

It could run:

gatk --java-options '--Xmx12g' Pileup 

Then gatk can be simply added as a conda dependency for Conpair.

Vlad