Is the a way to access argument tags in the arguments to a Qscript?
I have a script that takes a number of bam files as input and I would like to be able to tag them. i.e.
--input:whole-genome some_long_name.bam --input:exome a_different_bam.bam
In a walker I do this and then look up the tags by calling getToolkit().getTags(argumentValue), but this isn't available to a qscript. Is there a good way to do this?
Previously I have been running a command like this:
java -jar /path/GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R /path/human_g1k_v37.fasta \ -et NO_ET \ -K /path/key \ -out_mode EMIT_ALL_SITES \ --input_file /path/bam \ -L /path/intervals \ -gt_mode GENOTYPE_GIVEN_ALLELES \ --alleles /path/vcf \ --dbsnp /path/dbsnp_135.b37.vcf \ -o /path/my.vcf
But I was reading the documentation again and I read this statement: GENOTYPE_GIVEN_ALLELES only the alleles passed in from a VCF rod bound to the -alleles argument will be used for genotyping
Which lead me to believe that there wasn't a need to include the lines: --input_file /path/bam \ -L /path/intervals \
because it would be redundant. But when I try to run without those line I get back an error message: Walker requires reads but none were provided.
Can you give an explaination as to why both of those lines AND GENOTYPE_GIVEN_ALLELES would be needed?