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Can I merge SAM files?
You have two options wiht samtools: samtools cat – work on for bam and cram files, and the sequence dictionary of the files being concatenated need to be identical. samtools merge – work for sam, bam and cram, takes as input a sorted files, and outputs a sorted file.
What does samtools merge do?
Merge multiple sorted alignment files, producing a single sorted output file that contains all the input records and maintains the existing sort order. The output file can be specified via -o as shown in the first synopsis.
What is read group in BAM file?
Read groups are identified in the SAM/BAM /CRAM file by a number of tags that are defined in the official SAM specification. These tags, when assigned appropriately, allow us to differentiate not only samples, but also various technical features that are associated with artifacts.
Can BAM files be merged?
MergeSamFiles (Picard) Follow. Merges multiple SAM and/or BAM files into a single file. This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similarl to the “merge” function of Samtools (http://www.htslib.org/doc/samtools.html).
How do you merge with different read groups?
Sorry, how do you merge with different read groups, there doesn’t seem to be an option for that using merge bam files in SAM tools? Thanks. I’ll give it a go.
What do you mean by Merge in SAMtools?
samtools merge – merges multiple sorted input files into a single output.
How to add read groups to BAM files?
First run the tool “NGS: Picard (beta) -> Add or Replace Groups” to add read groups to each of your BAM files. Second, run the tool “NGS: SAM Tools -> Merge BAM Files”.
When to combine multiple @ RG headers with the same ID?
When several input files contain @RG headers with the same ID, emit only one of them (namely, the header line from the first file we find that ID in) to the merged output file. Combining these similar headers is usually the right thing to do when the files being merged originated from the same file.