BWA-mem alignment

0

Hi!

I'm doing an alignment to a reference genome by using the bwa-mem algorithm but I'm obtaining a bam file in which all the data seems to appear in the Chr1 as I see in IGV and the bam file obtained. The code that I'm using is:

threads=$SLURM_JOB_CPUS_PER_NODE

bwa index ./GRCh37.p13_alignCNVs.fasta

bwa mem -t $threads ./GRCh37.p13_alignCNVs.fasta ./NA12878_1.fastq ./NA12878_2.fastq |
samtools view -S -b - |
samtools sort - -o sample_sorted.bam
samtools index sample_sorted.bam


Data


Genomics


WGS

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