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?
In the below GATK command:
t he -L20 and -known do the same as in the previous command. Thank you .
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?
Code:
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.
Code:
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
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