Greetings everyone,
I have a quite large BAM-File after an alignment with bwa. My question is pretty general:
Is there a tool to extract some reads (by read name or row index) from a BAM-file?
I already did this once on the fastq files, but it would be really helpful to work directly on the BAM-file so I don't have to do all the preceding steps (alignment, conversion from SAM to BAM, sorting, removing of duplicate reads etc.) again.
I could not find any tool yet, that is able to read and write BAM-file. Does anyone have experience with Rsamtools, a Bioconductor package to read BAM-files into R? I couldn't find any way to export the data from R back into a BAM-file. If Rsamtools could write BAM-files it would be perfect. I'm looking for something similar.
I would be very great if someone knows such a tool or can give any advice on how to get a subset of my aligned reads without having to repeat the whole alignment procedure and post-processing.
Thanks in advance.
I have a quite large BAM-File after an alignment with bwa. My question is pretty general:
Is there a tool to extract some reads (by read name or row index) from a BAM-file?
I already did this once on the fastq files, but it would be really helpful to work directly on the BAM-file so I don't have to do all the preceding steps (alignment, conversion from SAM to BAM, sorting, removing of duplicate reads etc.) again.
I could not find any tool yet, that is able to read and write BAM-file. Does anyone have experience with Rsamtools, a Bioconductor package to read BAM-files into R? I couldn't find any way to export the data from R back into a BAM-file. If Rsamtools could write BAM-files it would be perfect. I'm looking for something similar.
I would be very great if someone knows such a tool or can give any advice on how to get a subset of my aligned reads without having to repeat the whole alignment procedure and post-processing.
Thanks in advance.
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