first all, I am new in bioinformatics, I came from the High Performance Computing world. I am trying the bwa tool to check it performance and I am facing the following problem. If I execute bwa mem paired in sequential mode (this is, without the -t option), then later I execute the program again with the same input and with 8 threads ( -t 8 ) the resulting sam file has a lot of differences with the sequential one. These are all the steps I did.
1.- Download the reference from: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
2.- Create the index with bwa index -a bwtsw
3.- Download the reads from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12750/sequence_read/ERR000589_1.filt.fastq.gz and ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12750/sequence_read/ERR000589_2.filt.fastq.gz
4.- Execute bwa in sequential mode with bwa mem Reference ERR000589_1.filt.fastq ERR000589_2.filt.fastq > ExitSequential.sam (I previously unzipped the input files)
5.- Same as in point 4 but adding the -t 8 option
6.- I made a diff between the exits and I found a lot of differences in the FLAG, MAPQ, RNEXT and PNEXT fields of the sam files
Can somebody please help me with this? Thanks in advance.
The bwa version is 0.7.12-r1039 from github