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I performed a genomic capture (Agilent technologie, SureSelect Target Enrichment System for Illumina Paired-end Sequencing) with paired tumoral and constitutional DNAs.
I created a .bam file for each both. I used bwa for alignment and samtools to create my bam file.
Now, I would like to call somatic mutations from these pair of samples (Tumoral vs Germline) with samtools (example of commands : samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf ). The goal is to eliminate all the commons mutations present in the two samples in order to keep only the somatic mutations.
Anybody can help me to understand how to realize this step?
What is the command for samtools ?
Thank you very much for your help
Sam64
I created a .bam file for each both. I used bwa for alignment and samtools to create my bam file.
Now, I would like to call somatic mutations from these pair of samples (Tumoral vs Germline) with samtools (example of commands : samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf ). The goal is to eliminate all the commons mutations present in the two samples in order to keep only the somatic mutations.
Anybody can help me to understand how to realize this step?
What is the command for samtools ?
Thank you very much for your help
Sam64
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