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Forum: Bioinformatics 06-19-2019, 06:25 AM
Replies: 0
Views: 323
Posted By dfermin315
Correct options for CNVnator

Greetings,

I'm trying to run CNVnator on a cohort of ~300 BAM files.

For testing purposes I'm trying to run it on just 3 BAM files first.
Here are the commands I'm running:


export...
Forum: Bioinformatics 06-01-2018, 04:32 AM
Replies: 2
Views: 1,282
Posted By dfermin315
Thanks for pointing me to that post! I'm still...

Thanks for pointing me to that post!
I'm still having issues but I'll work with the suggested command there.
Forum: Bioinformatics 05-30-2018, 01:20 PM
Replies: 2
Views: 1,282
Posted By dfermin315
Fixing BAM file header. Getting "truncated file. Aborting" error

Hello.

I have a BAM file that I need to filter and then update the header for.

These are my commands:


samtools view -@ 32 -h -b -f 2 -T /data/hs37d5.fa \
-o samp1234.clean.bam \
...
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