SAM file quality check without converting into BAM
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5.4 years ago
vaish01kv • 0

How to check if the sequences have aligned properly using SAM file before converting it into BAM.? Are there any tools which can read/process SAM file?

TIA.

Alignment SAM • 2.8k views
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Why wouldn't you convert it to bam?

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To check if the reads are properly aligned.

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As you hopefully do not do that by eye, it does not matter what format the file is. BAM is preferred as mentioned below.

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I couldn't generate BAM as the process stops when it reaches 57GB of BAM file saying broken pipe. I wanted to check if the generated SAM file is complete.

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Please share the command. BAM is smaller than SAM. THe simplest command is

aligner... | samtools view -o out.bam

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Thank you!! I generated SAM using bwa mem. My fastq files are large. 24 GB zipped file each reads, which ended up generating 259GB of sam file. I have used the above mentioned command now. It says 25hrs of run (Approx).

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Thank you so much. But the input file is BAM for the link you have mentioned.

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Please read the docs:

This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.

Still, BAM is preferred as it is compressed and index-able.

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