I need to fetch 2 BAM files from an HTTP server and I only need 'chr1' so I'm attempting to use:
samtools view -h http://cdna.eva.mpg.de/denisova/alignments/T_hg19_1000g.bam chr1 chr1.bam
for each file but I'm getting an error:
[knetseek] SEEKEND is not supported for HTTP. Offset is unchanged.
This is also inhibiting me from indexing the files.
In the end these 2 chromosomes will be used to compare indels/SNPs using IGV or whichever program we choose at that time. If anyone has some tips or shortcuts for a beginner I'd truly appreciate it.
Edit: Not FTP. It's a HTTP server
•
written
by
Khoops66 •
This command works on my system (Linux 64Bit):
samtools view -h http://cdna.eva.mpg.de/denisova/alignments/T_hg19_1000g.bam chr1
This doesn't extract it to a new file thought, right? Regardless, I'm still getting a 'SEED_END' error. Could it have something to do with Cygwin?
I apologize for my ignorance, all I need to accomplish is compare indels/SNPs between to BAM chromosomes.
This doesn't extract it to a new file thought, right? Regardless, I'm still getting a 'SEEK_END' error. Could it have something to do with Cygwin? I apologize for my ignorance, all I need to accomplish is compare indels/SNPs between to BAM chromosomes
this command uses the operating systems' network library so everything is possible, I just noticed that I also get the message but after that the data is shown just fine. I don't think this is an error just a warning.
Log in to answer this question.
If it's HTTP, it's not a FTP server :) Are we allowed to know the URL?
Yes! The file is here http://cdna.eva.mpg.de/denisova/alignments/
it's the hg19 file.