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Update README.md
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jfnavarro authored Nov 7, 2020
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Expand Up @@ -14,7 +14,7 @@ There are 2 pipelines and 2 tools:

**dna_pipeline.py** processes DNA data and generates a list of unified
filtered and annotated somatic variants.
The variant callers are Mutect2, Strelka, Varscan and SomaticSniper and both indels and SNPs are
The variant callers are Mutect2, Strelka2, Varscan and SomaticSniper and both indels and SNPs are
reported. Annotation is performed using Annovar.
The pipeline uses trim-galore to trim, bwa-men to align and follows GATK4 best practices.
The pipeline also performs HLA predictions with HLA-LA (tumor and normal).
Expand Down Expand Up @@ -71,9 +71,9 @@ Other files:
- combined_calls.vcf
- tumor_dedup.bam
- normal_dedup.bam
- *fastqc*
- bamQC_Normal
- bamQC_Tumor
- fastqc files
- bamQC_Normal folder
- bamQC_Tumor folder

**rna_pipeline.py**
- annotated.hgXX_multianno.vcf (annotated and combined germline variants)
Expand All @@ -83,8 +83,8 @@ Other files:
Other files:
- combined_calls.vcf
- sample_dedup.bam
- *fastqc*
- bamQC
- fastqc files
- bamQC folder

**merge_results.py**
- overlap_final.txt (all the DNA and RNA variants collapsed and filtered with useful information and epitopes)
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