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HaplotypeCaller can not emit bamout in multi-threaded mode

Lisa0508Lisa0508 Ann Arbor, MIMember

Hi all,
I used multi-threading mode on HaplotypeCaller hoping to save some time. But seemed like bamout can not be emitted in multi-threading mode. I searched the answers. But I am still not sure if the latest 3.4-46 version can support multi-threading with bamout. BTW, I am still using the old 3.3-0 version. If you say yes, now 3.4 version can support multi-threading bam, then I will ask the computing core to update gatk for me. Or maybe I just delete the bamout option to save some time. But I really prefer not to do so because I need to check the depth and coverage of mapping results actually finally used for variant calling.
My command line:
java -Xmx12g -jar $GATK_JARS/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-nct 12 \
-R human_g1k_v37.fasta \
--dbsnp dbsnp_138.b37.vcf \
-I recal_realigned_b37.dedup.sorted.bam \
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 20 \
--emitRefConfidence GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000 \
-o raw_var_TKDOME.g.vcf \
-bamout force_bamout_TKDOME_b37.bam -forceActive -disableOptimizations
BTW, is it necessary to add --variant_index_type LINEAR and --variant_index_parameter 128000 in Version 3.3?
Thank you very much!

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