@@ -25,8 +25,9 @@ Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17
...
@@ -25,8 +25,9 @@ Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17
We perform alignment using both human and mouse reference genomes in order to perform reads disambiguation using [disambiguate](https://pubmed.ncbi.nlm.nih.gov/27990269/) and discard reads from human mapping that belong to mouse cells.
We perform alignment using both human and mouse reference genomes in order to perform reads disambiguation using [disambiguate](https://pubmed.ncbi.nlm.nih.gov/27990269/) and discard reads from human mapping that belong to mouse cells.
`python disambiguate.py -a bwa -s SampleID 02-Alignment_human/SampleID.dedup_reads_rehead_recal.bam 02-Alignment_mouse/SampleID.dedup_reads_mouse_recal.bam`
```
python disambiguate.py -a bwa -s SampleID 02-Alignment_human/SampleID.dedup_reads_rehead_recal.bam 02-Alignment_mouse/SampleID.dedup_reads_mouse_recal.bam
```
# Variant calling #
# Variant calling #
For variant calling analysis we opted for Mutect2 algorithm (more sensitive for somatic variants identification) in tumor-only mode.
For variant calling analysis we opted for Mutect2 algorithm (more sensitive for somatic variants identification) in tumor-only mode.
