Hello expert members,
I would like to get your advice regarding BWA alignment options. I found in the bwa manual that it uses only two read files for paired-end and one read file for single-end data at a time. However, I have 3 genotypes (each has two fastq files) to identify and compare SNPs among them. According to the BWA guideline, I used two (read1.fastq and read2.fastq) files of one genotype at a time to make alignment against the reference genome using the following command line:
bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered > aln-BH.sam
bwa mem ref.fasta Cyp_1.fastq_filtered Cyp_2.fastq_filtered > aln-Cyp.sam
bwa mem ref.fasta SR_1.fastq_filtered SR_2.fastq_filtered > aln-SR.sam
Now I have 3 *.sam files for the 3 genotypes for SNPs variant calling. My question - is it possible to use all 6 fastq files from 3 genotypes in the single command to get a single *.sam file like below:
bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered Cyp_1.fastq_filtered Cyp_2.fastq_filtered SR_1.fastq_filtered SR_1.fastq_filtered > aln-bwa.sam
Thank you so much for taking your valuable time and I would appreciate your advice.
Thanks
Shofi
I would like to get your advice regarding BWA alignment options. I found in the bwa manual that it uses only two read files for paired-end and one read file for single-end data at a time. However, I have 3 genotypes (each has two fastq files) to identify and compare SNPs among them. According to the BWA guideline, I used two (read1.fastq and read2.fastq) files of one genotype at a time to make alignment against the reference genome using the following command line:
bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered > aln-BH.sam
bwa mem ref.fasta Cyp_1.fastq_filtered Cyp_2.fastq_filtered > aln-Cyp.sam
bwa mem ref.fasta SR_1.fastq_filtered SR_2.fastq_filtered > aln-SR.sam
Now I have 3 *.sam files for the 3 genotypes for SNPs variant calling. My question - is it possible to use all 6 fastq files from 3 genotypes in the single command to get a single *.sam file like below:
bwa mem ref.fasta BH_1.fastq_filtered BH_2.fastq_filtered Cyp_1.fastq_filtered Cyp_2.fastq_filtered SR_1.fastq_filtered SR_1.fastq_filtered > aln-bwa.sam
Thank you so much for taking your valuable time and I would appreciate your advice.
Thanks
Shofi
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