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Phasing a whole genome

wesleyvanleewesleyvanlee The netherlandsMember

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.)?

Wesley.

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