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Thank you for your patience!
I'm using IndelRealigner, and it seems to take long time, from 5 to 8h, I have a strange sensation that I may not put the right commands but I'm not sure. Previously of what I show below I have Marked duplicates with MarkDuplicates.
/home/Programas/samtools-0.1.19/samtools index /local/ktroule/SNPiR/Panc047/accepted_hits_RG_Reordered_deduplicated.bam java -Xmx20g -jar /home/Programas/GATK-3.1-1-g07a4bf8/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa -I /local/SNPiR/Panc042/accepted_hits_RG_Reordered_deduplicated.bam --unsafe ALLOW_N_CIGAR_READS --known /local/Referencias/HG19/Mills_and_1000G_gold_standard.indels.hg19.vcf -o /local/SNPiR/Panc042/Panc042_indel.intervals java -Xmx20g -jar /home/Programas/GATK-3.1-1-g07a4bf8/GenomeAnalysisTK.jar -T IndelRealigner --targetIntervals /local/SNPiR/Panc042/Panc042_indel.intervals -R /local/Referencias/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa --unsafe ALLOW_N_CIGAR_READS -I /local/SNPiR/Panc042/accepted_hits_RG_Reordered_deduplicated.bam -o /local/SNPiR/Panc042/accepted_hits_RG_Reordered_deduplicated_Realigned.bam
This is not really about an error, but about If the program takes that long and about if the parameters I have used are the rights ones, as I have seen that few ones use the downsampling.
Finally, if I have not read wrongly InderRealigner does not support multithread, at least not directly from the program.
thanks for yor time.