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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How to use bwa mem for paired-end Illumina reads
we would like to use the bwa mem algorithm for the alignment of paired-end (100 bp) Illumina reads and variant calling
with GATK. Unfortunately there are some problems understanding the command description.
Do I need to use the -p and [mates.fq] options for paired-end reads?
And what about simply using the command below?
bwa mem -M -t 16 ref.fa read1.fq read2.fq > aln.sam
Command description (http://bio-bwa.sourceforge.net/bwa.shtml):
"If mates.fq file is absent and option -p is not set, this command regards input reads are single-end. If mates.fq is present, this command assumes the i-th read in reads.fq and the i-th read in mates.fq constitute a read pair. If -p is used, the command assumes the 2i-th and the (2i+1)-th read in reads.fq constitute a read pair (such input file is said to be interleaved). In this case, mates.fq is ignored. In the paired-end mode, the mem command will infer the read orientation and the insert size distribution from a batch of reads.
The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for long sequences. However, some tools such as Picard’s markDuplicates does not work with split alignments. One may consider to use option -M to flag shorter split hits as secondary."
We appreciate your help!