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Parse error at line.....

Hi I am trying to convert sam file to bam file and encountered this problem . Not sure how to troubleshoot, Can someone help please as I am very new to bioinformatics 

samtools view -S -b aln2.sam > aln2.bam
[W::sam_read1] Parse error at line 753646
[main_samview] truncated file.
alignment
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updated by lieven.sterck lieven.sterck • written by priscilladraj • priscilladraj

1 answer

The file is corrupted, repeat alignment. That is the most robust option. When you do pipe directly into samtools.

alignment_code (...) | samtools view -o aln2.bam
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written by ATpoint ATpoint

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

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written by GenoMax GenoMax

Hey thanks genomax . I am still new so this small information is also useful for me :D

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written by priscilladraj • priscilladraj

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