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About population indel calling
Recently I have 2444 samples to perform population INDEL calling. The samples are all whole-exome sequecing with average depth ~45X. I called these 2444 samples simultaneously using 2444 reduced BAMs, and used 4 CPU threads. Here is my script:
**java -Xms2g -Xmx8g -jar /path/GenomeAnalysisTK-2.2-8-gec077cd/GenomeAnalysisTK.jar \
-R /path/hg19/ucsc.hg19.fasta \
-T UnifiedGenotyper -nct 4 \
-I /path/reduced.bam.list --dbsnp dbsnp_135.hg19.vcf \
-o chr7.raw.vcf -stand_call_conf 30.0 -dcov 600 \
-glm INDEL -A HomopolymerRun -A InbreedingCoeff -A IndelType -l INFO \
-L chr7_ex200.bed **
It is too slow. For example, there is 6096403 bp region in chr7_ex200.bed. It costs about 7days.
INFO 13:46:13,480 ProgressMeter - chr7:48559385 4.34e+06 48.3 h 11.1 h 28.6% 7.0 d 5.0 d
INFO 13:47:19,172 ProgressMeter - chr7:48619576 4.34e+06 48.4 h 11.1 h 28.6% 7.0 d 5.0 d
INFO 13:48:26,270 ProgressMeter - chr7:48655039 4.35e+06 48.4 h 11.1 h 28.7% 7.0 d 5.0 d
INFO 13:49:41,206 ProgressMeter - chr7:48684363 4.35e+06 48.4 h 11.1 h 28.7% 7.0 d 5.0 d
How could I speed up my population indel calling? Could someone give me some suggestion?
Thanks in advance.