mapping form different lane

Question

[Siavash Salek Ardestani]

Hi to all I have 4 lanes (whole genome seq) from 1 sample, I want to know how can I mapping these sequence?

Answer 1

[swbarnes2]

Concatenate all your read 1 fastq.gz samples together, and all your read 2 fastq samples together, then align.

Or, do the alignments separately, and use samtools merge to make one combined .bam from the 4 separate .bams

Answer 2

[h.mon]

Using any one of a number of mappers, like BWA, Bowtie2, HISAT2, STAR, and so on - the appropriate mapper will depend on what kind of data you have, and downstream analysis you want to perform.

Do you have particular concerns? What exactly do you want to do? Map all files to into a single bam?

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[Siavash Salek Ardestani]

No, I mean, I have 4 lanes that Each one included a forward and a reverse read so In total I have 8 fastq.gz files. I do not know how can I do mapping? because, BWA accept only two inputs ( a forward and a reverse read) not 8 inputs.

[h.mon]

What are you going to do downstream? For example, for variant calling, it is important (at least for GATK) to add read groups for each lane separately, so I would suggest mapping each pair of files separately, using the -R flag to add appropriate read group information. You can then merge with samtools or Picard.

If you want to map all files in one step, you can use process substitution:

bwa mem index_name <(cat *_R1.fastq.gz) <(cat *_R2.fastq.gz)

[Siavash Salek Ardestani]

I want for SNP discovery. so if I want to map all files in one step then I faced problems in GATK? is it true?