Hi I'm trying to follow a work flow and I'm confused by instruction.
This is what the instruction says,
- Map reads with bwa as single end sequences then combine single reads into one file
How does one combine single reads into one file? What tried so far is this.
bwa mem -t 4 hg19 Kf_1.fq.gz > Kf_1.sam; bwa mem -t 4 hg19 Kf_2.fq.gz > Kf_2.sam;
I then tried to combine the sam file with picard,
java -jar picard.jar MergeSamFiles I=Kf_1.sam I=Kf_2.sam O=/sc/snpir.out/KF.sam
but this does not work because I assume headers are completely the same for both files? I get this error here,
Cannot add sequence that already exists in SAMSequenceDictionary:
Does anyone have an idea how I can go about this? perhaps I'm not reading the instruction correctly??
thanks in advance!