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Bwa command line parameters at 5 dollars pipeline

Dear colleagues, I see
bwa_commandline="bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta"
at 5 dollars pipeline but bwa does wrong things this way.
When I use "-p" parameter it does produce only half of reads aligned. For example:
/Users/software/bwa-0.7.17/bwa mem -K 100000000 -v 3 -t 1 -Y -R '@RG\tLB:RG_LB1\tSM:RG_SM\tPM:E00593\tPU:HGC7FCCXY.1\tID:HGC7FCCXY.1.NGTCAACA\tPL:ILLUMINA' /Users/pipeline/5dollar/Homo_sapiens_assembly38.fasta /Users/tmp/genome.GenomeAnalysisTest/1.R1.1.fastq /Users/tmp/genome.GenomeAnalysisTest/1.R2.1.fastq > /Users/tmp/genome.GenomeAnalysisTest/1.1.sam
cat 1.1.sam | grep -v '@' | wc -l
202

/Users/software/bwa-0.7.17/bwa mem -K 100000000 -p -v 3 -t 1 -Y -R '@RG\tLB:RG_LB1\tSM:RG_SM\tPM:E00593\tPU:HGC7FCCXY.1\tID:HGC7FCCXY.1.NGTCAACA\tPL:ILLUMINA' /Users/pipeline/5dollar/Homo_sapiens_assembly38.fasta /Users/tmp/genome.GenomeAnalysisTest/1.R1.1.fastq /Users/tmp/genome.GenomeAnalysisTest/1.R2.1.fastq > /Users/tmp/genome.GenomeAnalysisTest/1.1.sam
cat 1.1.sam | grep -v '@' | wc -l
102

Could you comment on this and please also describe what "-Y" is for? (there is no such option at bwa manual).

Answers

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