Preprocessing .bam Files with samtools vs MELT

[Shilpa]

Hello MELT helpdesk,

Thank you so much for developing an amazing MEI discovery tool. It is also must faster than the other available tools. I have a basic doubt regarding preprocessing of .bam files.

This is the command suggested by MELT.

java –Xmx2G –jar MELT.jar Preprocess -bamfile name.sorted.bam -h reference.fa;

I have processed my bam files with

samtools sort bamout.bam bamin.bam

samtools index bamout.bam

Does it matter if I process it using "Melt's command" or by using samtools?

Thank you for your time.

[Sagar S]

Hi Shilpa,

This Google group has been inactive since 2022. The author has mentioned that no questions posted here will be answered by him.

I have been using MELT for a long time and thought I would add an answer to your question.

MELT Preprocess accepts a coordinate-sorted and indexed BAM file (like the one you have sorted using Samtools). What actually happens in the preprocessing step is that MELT collects discordant read pairs from the BAM file you input and stores them as sample.disc.bam, which speeds up the process of MELT IndivAnalysis. It is a required step if you are processing your samples using MELT-SPLIT.

Hope this helps.

Regards,
Sagar