Can Some One Explain These Gatk Unifiedgenotyper Commands And Difference In Terms Of Output Also

Question

[always_learning]

Can some one explain these GATK Unifiedgenotyper Commands and difference in terms of output also

This one is basically used for calling Dindel target

1) java -Xmx54g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -nt 16 -l INFO -R refGenomeFile -I fixed.bam -L exome_target_list -o indel.target.vcf -stand_call_conf 50.0 -S SILENT -D ${DBSNP} --max_alternate_alleles 1 -metrics ${resultDir}/${woId}-${sgId}.target.INDELmetrics -glm INDEL -A FisherStrand -A DepthOfCoverage -A AlleleBalance'

This one is used for calling all Dindel:

2) java -Xmx54g -jar GenomeAnalysisTK.jar \ -T UnifiedGenotyper -nt 16 -l INFO -R refGenomeFile \ -I fixed.bam -stand_call_conf 50.0 \ -S SILENT -o indel.vcf \ -D DBSN --max_alternate_alleles 1 \ -metrics INDELmetrics -glm INDEL -A FisherStrand -A DepthOfCoverage -A AlleleBalance'

Please help me in understanding these two !!

Answer 1

[Ashutosh Pandey]

I know this is not what you are looking for but GATK has well written documentation available at http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html

You should try to read it first. Also, commands you have mentioned have more than one parameters where they differ. No one would go through your commands and read all the parameters for you and then explain it to you. If you have a specific parameter you want to talk about please mention it below.