GATK command options

[cmccabe]

I just want to be sure that I am interpreting the below correct:

In this GATK command the -L 20 gives the chromosome 20 only and if all chromosomes were used then the -L can be removed.

The -known is only used if your organism has a file (maybe hg19 does, but I have to search). Is it a text file?

java -jar GenomeAnalysisTK.jar \ 
    -T RealignerTargetCreator \ 
    -R reference.fa \ 
    -I dedup_reads.bam \ 
    [B][B]-L 20 \ [/B][/B]       (chromomosome 20 only)
    [I]-known gold_indels.vcf \ [/I]   (optional) 
    -o realignment_targets.list

Expected Result

This creates a file called realignment_targets.list containing the list of intervals that the program identified as needing realignment within our target, chromosome 20.

The list of known indel sites (gold_indels.vcf) are used as targets for realignment. Only use it if there is such a list for your organism.

In the below GATK command:

java -jar GenomeAnalysisTK.jar \ 
    -T BaseRecalibrator \ 
    -R reference.fa \ 
    -I realigned_reads.bam \ 
    -L 20 \ 
    -knownSites dbsnp.vcf \ 
    -knownSites gold_indels.vcf \ 
    -o recal_data.table

t he -L20 and -known do the same as in the previous command. Thank you .

[HESmith]

"gold_indels.vcf" is a VCF; see here for the latest specification.

[WhatsOEver]

Concerning your question: No, "L" restricts the variant calling to a certain region (in your example chr20); "known" specifies a file containing known variants - these files contain variant info over the whole genome.

The Broad institute offers a resource bundle for hg19 which also include the known variants (https://www.broadinstitute.org/gatk/download/)

[cmccabe]

Thank you .