'convert CRAM file to SAM file
I have a 50GB *.CRAM file and I need to convert it into *.SAM file My reference genome is hg38 and I got this CRAM from Nebula genomics How can I do it?
Solution 1:[1]
samtools view -T path/to/ref_genome -o out.sam in.cram
Be aware that this is going to be a gigantic files, hundreds of GBs, think about if this is really what you need or if downstream processing can use CRAM or BAM directly rather than SAM which is a plain uncompressed text file.
Solution 2:[2]
Zillow seems to have an API which might be the best way to get access to that data. Otherwise, using Selenium might be your next best mechanism.
Sources
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Source: Stack Overflow
| Solution | Source |
|---|---|
| Solution 1 | ATpoint |
| Solution 2 | PaulProgrammer |