How can all BWA alignment get wrong mapping location?
I mapped using bwa, 2 paired end sequences from exome sequencing using this command:
bwa mem -t 10 -M -R '@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1' h19_index_bwa/h19 MM160301JR_1.fastq MM160301JR_2.fastq > MM160301JR2.sam
After viewing the bamfile on IGV, I notice that all reads are on wrong positions as its sequence does not match the reference, however reads are mapped correctly against itself. How can it be?
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May be obvious but thought I would ask. You have the correct genome build loaded in IGV, right?
turns out that no, I thought I mapped with hg19, but was not. I will leave this post and make the walk of shame