summary OfAllSmash

summary of all the wiki/issues for Smash:

Smash wiki

• Link to the original fast files for:

  • NA12878
  • NA18507
  • NA19240

• Link to Smash Download and QC

• Link to Smash Downloadable Material

  • Just links to the amazonaws

• A summary of which files belong to what sample

• Methodology we will use for the project.

  1. Downloading BAM files (whole genome sequencing data) from SMaSH data
  2. Extracting reads from coding exon regions (+/- 20 bp)
  3. Extracting truth variants from the same regions as step2
  4. Converting BAM back to fastq files
  5. Running Variant Calling pipeline
  6. Evaluating results

##Issues

Validating smash's bam files###

Summary of the different steps taken for the different files

• NA19240.bam

  1. `java -Xmx6g -jar ValidateSamFile.jar INPUT=NA19240.bam MODE=SUMMARY \`
     `VALIDATION_STRINGENCY=STRICT`
  
  2. ` java -Xmx6g -jar CleanSam.jar INPUT=NA19240.bam OUTPUT=NA19240_cleaned.bam `
    
  3. `java -Xmx6g -jar ValidateSamFile.jar INPUT=NA19240_cleaned.bam MODE=SUMMARY \`        
     `VALIDATION_STRINGENCY=STRICT` 
  
  4. ` java -Xmx6g -jar FixMateInformation.jar INPUT=NA19240_cleaned.bam \`
    `OUTPUT=NA19240_cleaned_fixed.bam VALIDATION_STRINGENCY=LENIENT \`
    `TMP_DIR=/Volumes/ `
  
  5. `java -Xmx6g -jar ValidateSamFile.jar INPUT=NA19240_cleaned_fixed.bam\ `
     ` MODE=SUMMARY VALIDATION_STRINGENCY=STRICT` 
     
  6. `samtools  view -b -L uscs_all_exons_sorted+-20.bed NA19240_cleaned_fixed.bam > NA19240_cleaned_fixed+-20.bam`
  
  7. `java -Xmx6g -jar ValidateSamFile.jar INPUT=NA19240_cleaned_fixed+-20.bam\ `
     ` MODE=SUMMARY VALIDATION_STRINGENCY=STRICT`
  
  8. `java -Xmx8g -jar FixMateInformation.jar INPUT=NA19240_cleaned_fixed+-20.bam \`
     `OUTPUT=NA19240_cleaned_fixed+-20_posiSrt.bam `
     `CREATE_INDEX=TRUE VALIDATION_STRINGENCY=STRICT SORT_ORDER=queryname `
  
  9. `java -Xmx8g -jar FixMateInformation.jar INPUT=NA19240_cleaned_fixed+-20.bam `
     `OUTPUT=NA19240_cleaned_fixed+-20_posiSrt.bam CREATE_INDEX=TRUE `
     `VALIDATION_STRINGENCY=STRICT SORT_ORDER=coordinate TMP_DIR=Seagate\ Exp/`
  

  10. samtofastaq

| File | ERROR INVALID INDEXING_BIN | ERROR INVALID MAPPING_QUALITY | ERROR MISMATCH FLAG_MATE_NEG_STRAND | ERROR MISMATCH FLAG_MATE_UNMAPPED | | :----: | :----: | :----: | :----: | :----: | :----: | | NA19240.bam | 58471 | 2009 | 13980965 | 2045 | |NA19240_cleaned.bam | 58471 | 0 | 13980965 | 2045 | |NA19240_cleaned_fixed.bam | 0 | 0 | 0 | 0 | |NA19240_cleaned_fixed+-20.bam| 0 | 0 | 0 | 21667367| |NA19240_cleaned_fixed+-20_posiSrt.bam | 0 | 0 | 0 | 21667367 |

• Contaminated_NA12878