Merge branch 'master' of github.com:hammerlab/isovar

README.md

@@ -14,7 +14,7 @@ Isovar assembles protein subsequences around mutations from cancer RNA-Seq data.
 ## Example
 
 ```sh
-$ isovar-protein-sequences.py  \
+$ isovar-protein-sequences  \
     --vcf somatic-variants.vcf  \
     --bam rnaseq.bam \
     --min-reads 2 \
@@ -51,3 +51,14 @@ Since we may not want to deal with *every* possible translation of *every* disti
 ## Sequencing Recommendations
 
 Isovar works best with high quality / high coverage mRNA sequence data. This means that you will get best results from >100M paired-end reads sequenced on an Illumina HiSeq from a library enriched with poly-A capture. The number of reads varies depending on degree of RNA degradation and tumor purity. The read length will determine the longest protein sequence you can recover, since Isovar's cDNA assembly only considers reads that overlap a variant. With 100bp reads you will be able to assemble at most 199bp of sequence around a somatic single nucleotide variant, and consequently only be to determine 66 amino acids from the protein sequence. If you disable the cDNA assembly algorithm then a 100bp read will only be able to determine 33 amino acids.
+
+## Commandline Tools
+
+* `isovar-protein-sequences`
+* `isovar-allele-counts`
+* `isovar-allele-reads`
+* `isovar-translations`
+* `isovar-reference-contexts`
+* `isovar-variant-reads`
+* `isovar-variant-sequences`
+