From Genome Analysis Wiki
Jump to navigationJump to search
100 bytes removed
, 23:35, 5 March 2016
Line 2: |
Line 2: |
| The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files | | The <code>bam2FastQ</code> option on the [[bamUtil]] converts a BAM file into FastQ files. This is necessary when only BAM files are delivered but a new alignment is desired. By converting BAM to FastQ files new alignments can be done using FastQ files |
| | | |
− | '''NOTE: This tool does not work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.''' | + | '''NOTE: Secondary and Supplementary reads are skipped when converting to FastQ. It assumes that there will only be 2 reads (the 2 primary mates) with the same read name that are not secondary or supplementary.''' |
| | | |
− | '''NOTE: This tool does not split reads into read group specific FASTQs. If you want Read Group specific FASTQ files, first run [[BamUtil: splitBam]] to first split the BAM into 1 BAM per Read Group. Then run bam2FastQ on each bam.''' | + | '''NOTE: Use the --splitRG option to split reads into read group specific FASTQs.''' |
| | | |
| == How to use it == | | == How to use it == |