SAM file quality check without converting into BAM
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.
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Ram
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vaish01kv •
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vaish01kv •
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https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.1.1/picard_sam_ValidateSamFile.php
Thank you so much. But the input file is BAM for the link you have mentioned.
Please read the docs:
Still, BAM is preferred as it is compressed and index-able.
Why wouldn't you convert it to bam?
To check if the reads are properly aligned.
As you hopefully do not do that by eye, it does not matter what format the file is. BAM is preferred as mentioned below.
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.
Please share the command. BAM is smaller than SAM. THe simplest command is
aligner... | samtools view -o out.bamThank 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).