SAM file quality check without converting into BAM

Question

[vaish01kv]

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.

[WouterDeCoster]

Why wouldn't you convert it to bam?

[vaish01kv]

To check if the reads are properly aligned.

[ATpoint]

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

[vaish01kv]

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.

[ATpoint]

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

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

[vaish01kv]

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).

[ATpoint]

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.1.1/picard_sam_ValidateSamFile.php

[vaish01kv]

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

[ATpoint]

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.