I have WGS data of 5 human samples from Illumina HiSeq 2500 platform with PE sequencing with read length 101bp. The average size of one sample .sam file is 260GB and I am ran following command to change .sam to .bam format:
/usr/local/samtools-1.2/samtools view -b ETH002102.bwa.sam > ETH002102.bwa.sam.bam
Is there any way to fasten this conversion as it normally taking approx. 18-20 hours?
My 2nd question is related with 'SORTING' of .bam file, for that purpose I ran the following command:
/usr/local/samtools-1.2/samtools sort -@ 14 -m 5000000000 -T /tmp/ETH002102.bwa.sam.sort -o ETH002102.bwa.sam.sort.bam ETH002102.bwa.sam.bam
I also tried
-m 5G but I am not able to get the output. The command run for few minutes and then automatically killed by the clusters. I am not sure where is the error so it would be great if somebody will help me in giving correct command to run on clusters in multiples cores of a node (e.g. here I gave 14 as I had 16) i.e. in parallel mode. Since I am new in this area and doing such work for the first time so any help will be highly appreciated.
Thanks and Regards,