Hi,
I have sequence read data of 3 particular genes of Human.
I know their location on reference genome and so I retrieved their sequences and made another fasta file with regular header (>seq_name) and following concatenated three sequence without anything else.
My raw read file is of 18GB (paired end,Illumina). When I map them to custom reference (using BWA-SAMtools) I get Bam file of 8GB (Forward-Reverse merged). These all steps takes few minutes to few hours on my workstation. My BAM file index is only 36KB. When I input this BAM file in 'samtools pileup -vcf', it keeps running more than 3 days and the output file size is around 1.1GB. Its still running and I dont understand why it takes so much time? Another matter is when I checked output file after first day, it was 900MB, then on second day it was 1 GB and on third day its 1.1GB. I already killed this process before 7-8 days (because of same behavior) and restarted it. Please help me to understand why it is happening so? (there is no any error message on any of the steps)
Thanking you in advance...
I have sequence read data of 3 particular genes of Human.
I know their location on reference genome and so I retrieved their sequences and made another fasta file with regular header (>seq_name) and following concatenated three sequence without anything else.
My raw read file is of 18GB (paired end,Illumina). When I map them to custom reference (using BWA-SAMtools) I get Bam file of 8GB (Forward-Reverse merged). These all steps takes few minutes to few hours on my workstation. My BAM file index is only 36KB. When I input this BAM file in 'samtools pileup -vcf', it keeps running more than 3 days and the output file size is around 1.1GB. Its still running and I dont understand why it takes so much time? Another matter is when I checked output file after first day, it was 900MB, then on second day it was 1 GB and on third day its 1.1GB. I already killed this process before 7-8 days (because of same behavior) and restarted it. Please help me to understand why it is happening so? (there is no any error message on any of the steps)
Thanking you in advance...
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