Write out sequence read data (for filtering, merging, subsetting etc)
java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input1.bam -I input2.bam -o output.bam --read_filter MappingQualityZero // Prints the first 2000 reads in the BAM file java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.bam -n 2000 // Downsamples BAM file to 25% java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.bam -dfrac 0.25
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Outputs | |||
| --out  -o | stdout | Write output to this BAM filename instead of STDOUT | |
| Optional Parameters | |||
| --number  -n | -1 | Print the first n reads from the file, discarding the rest | |
| --platform | NA | Exclude all reads with this platform from the output | |
| --readGroup | NA | Exclude all reads with this read group from the output | |
| --sample_file  -sf | [] | File containing a list of samples (one per line). Can be specified multiple times | |
| --sample_name  -sn | [] | Sample name to be included in the analysis. Can be specified multiple times. | |
| Optional Flags | |||
| --simplify  -s | false | Simplify all reads | |