How to check the integrity of BAM and FASTQ files after conversion

[zhuchcn]

Hi SRA team, I have a question of how to check the integrity of the BAM or FASTQ files. The .sra.vdbcache files were downloaded using prefetch and validated using vdb-validate. But how can I check whether the extraction of BAM or FASTQ files from .vdbcache was complete and did not fail in the middle?

[klymenko]

Use vdb-validate to validate sra file.

[zhuchcn]

Use vdb-validate to validate sra file.

vdb-validate validates the sra file, yes. But when I use sam-dump to extract the SAM, how can I validate the SAM? My question is how can we find out if the sam-dump stopped in the middle and yielding a truncated SAM/BAM? This can still happen even when the SRA file is valid.

[klymenko]

Check the exit code of sam-dump or fasterq-dump.

[zhuchcn]

It will be great if some additional information can be shown. For example, showing the total reads that sam-dump prepares to extract, then users can count the reads in the output BAM files to check if they match.