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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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Correct use of BWA MEM? #52

Closed avanbeelen closed 1 year ago

avanbeelen commented 1 year ago

Hi,

To the author, is it possible to share the code on how to map reads to a hs37d5.fa using BWA MEM, please?

At the moment, I am mapping my reads like this:

 bwa mem \
            -t 60 \
            -Y \
            -q 50 \
            -R '@RG\\tID:test2\\tSM:test2}\\tPL:Illuminua\\tLB:lib2}\\tPU:unit1' \
            -t .temp/ /\
            hg19/hs37d5.fa \
            small_R1.fastq.gz \
            small_R2.fastq.gz} 2> log_1.txt | \
samtools view -@ 60 -Sb - 2> log_2.txt > mapped.bam

The reason why I need this is that I am trying to solve an error, and I am assuming the mapping part is incorrect.

It would be highly appreciated.

Best regards

avanbeelen commented 1 year ago

Found it:

bwa mem -t 16 -M -R @RG\tID:H7LH3CCXX_6\tPL:ILLUMINA\tSM:FR05812606\tCN:kccg /short/gd7/resources/gatk-resource-bundle/2.8/b37/human_g1k_v37_decoy.fasta /g/data2/gd7/research/andmin/NATA/reprod/r2/fastqs/H7LH3CCXX_6_150209_FR05812606_Human__R_150203_DAVMIL1_FGS_M001_R1.fastq.gz /g/data2/gd7/research/andmin/NATA/reprod/r2/fastqs/H7LH3CCXX_6_150209_FR05812606_Human__R_150203_DAVMIL1_FGS_M001_R2.fastq.gz