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Phasing a whole genome
Hello GATK team,
I am trying to phase data from WGS (Whole Genome Sequencing). The VCF contains 4.5milion variants. I am running GATK with the following command:
java -Xmx200g -jar GenomeAnalysisTK.jar -T ReadBackedPhasing -V R13-3.HS37.aln.normalized.toplevel-chrMT.vcf -R ref_hg19.fasta -I R13-3.HS37.toplevel.aln.bam -o R13-3_phased -maxSites 10 -phaseThresh 100.0
However, this will take way to long as you can see in the following output:
INFO 15:49:09,871 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 15:49:09,872 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 15:49:39,873 ProgressMeter - chr1:1034093 654657.0 30.0 s 45.0 s 0.0% 24.9 h 24.9 h INFO 15:50:39,874 ProgressMeter - chr1:1519229 1126294.0 90.0 s 79.0 s 0.0% 50.9 h 50.9 h INFO 15:51:39,875 ProgressMeter - chr1:2610117 2213313.0 2.5 m 67.0 s 0.1% 49.4 h 49.4 h INFO 15:52:39,876 ProgressMeter - chr1:2634141 2228357.0 3.5 m 94.0 s 0.1% 68.6 h 68.5 h INFO 15:53:39,877 ProgressMeter - chr1:2779797 2325732.0 4.5 m 116.0 s 0.1% 83.5 h 83.4 h INFO 15:54:39,878 ProgressMeter - chr1:3772721 3323905.0 5.5 m 99.0 s 0.1% 75.2 h 75.1 h INFO 15:55:39,879 ProgressMeter - chr1:4327377 3730321.0 6.5 m 104.0 s 0.1% 77.5 h 77.4 h INFO 15:56:39,880 ProgressMeter - chr1:4820798 4221553.0 7.5 m 106.0 s 0.2% 80.3 h 80.1 h INFO 15:57:39,886 ProgressMeter - chr1:5880473 5269727.0 8.5 m 96.0 s 0.2% 74.6 h 74.4 h
Is there a recommended set of arguments that can speed up this process significantly (e.g by skipping low quality sites, spots that are computationally intensive etc.)?