Previously this option was required if input was in SAM format, but now the correct format is automatically detected by examining the first few characters of input. etc." to feed the multithread?Īdditionally, I am using cluster computing, that I could apply for multiple nodes and then multiple processors for each node. INT, -threads INT Number of BAM compression threads to use in addition to main thread 0.-S Ignored for compatibility with previous samtools versions. ![]() ![]() Or like what said, need to split the bam file manually like "chr1:1-XX chr2:1-YY. When you talked about "flagstat will multithread well", do you mean it works well anyhow? It’s main function, not surprisingly, is to allow you to convert the binary (i.e. samtools view The samtools view command is the most versatile tool in the samtools package. The correct solution is to so as you say - batching up portions of the file to compute stats independently and then merge at the end. samtools view 1:33000000-34000000 wc -l. Unfortunately samtools stats spends a long time in the main thread so giving it more threads only speeds up a small portion of the total work load. If the command itself has a very fast main thread - eg "samtools flagstat" is dominated by decode or encode - then it'll multithread well. ![]() Every command has the capability to use threads for decoding and encoding of BAM and CRAM, but only a few also use the thread pool for others things ("samtools sort" is perhaps the only one).
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