Morning,
I´m using HaplotypeCaller program spliting by chromosomes in sheep genome.
On 22 chromosomes the process has been completed correctly, but on the others there have been several errors. The next paragraph is the command used for all 158 samples. We use nodes of 16 cores (-ntc 16) and 32 Gb of memory RAM.
java -Xmx28g -Djava.io.tmpdir=/scratch/dpaule_1/dpaule_1_3/tmp -jar /home/dpaule_1/COMUNES/WGS_software/gatk/3.8.0/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/dpaule_1/
COMUNES/reference_genome/reference_genome_Oar-v3.1-r90_toVariantCalling/Ovis_aries_v3.1-r90.fa -L 9 -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AFS32_SRR501853/AFS32_SRR50
1853_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AFS33_SRR501871/AFS33_SRR501871_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AU
MEHM000000000001/AUMEHM000000000001_recal_reads.bam -I
/home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AUMEHM000000000002/AUMEHM000000000002_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AUMEHM000000000003/AUMEHM000000000003_recal_reads.bam -I /home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AUMEHM000000000004/AUMEHM000000000004_recal_reads.bam -I
home/dpaule_1/dpaule_1_3/HECTOR/resultados_WGS_20171128_1704/AUMEPM000000000005/AUMEPM000000000005_recal_reads.bam....