How to find LB from fastq to create a read group?
I need to add the information about LB in the reads groups to mount using bwa, but I don't know how to do it. Can someone help me?
Hello I need help in getting read group info for performing alignment using BWA-MEM2. I read previous post (https://www.biostars.org/p/280837/) on read-group info, where a shell …
Hi Guys, While running GATK, I am getting ERROR MESSAGE: **SAM/BAM/CRAM file bwa/aln-SRR13785703.bam is malformed. Please see https://software.broadinstitute.org/gatk/documentation/article?id=1317for more information. Error details: SAM file doesn't …
I assembled an exome using the following command: bwa mem -t 12 -B 4 -O 6 -E 1 -M -R '@RG\tID:SRR1517898\tSM:HG00096\tPL:ILLUMINA' /home/ims.santos06/reference/hg38.fa /home/ims.santos06/fastq/SRR1517898_1.fastq.gz /home/ims.santos06/fastq/SRR1517898_2.fastq.gz | …