Extracting Two Bam Files And Indexing Them To Compare Indels

Question

[Khoops66]

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

[Neilfws]

If it's HTTP, it's not a FTP server :) Are we allowed to know the URL?

[Khoops66]

Yes! The file is here http://cdna.eva.mpg.de/denisova/alignments/

it's the hg19 file.

Answer 1

[Istvan Albert]

This command works on my system (Linux 64Bit):

samtools view -h http://cdna.eva.mpg.de/denisova/alignments/T_hg19_1000g.bam chr1

[Khoops66]

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.

[Khoops66]

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

[Istvan Albert]

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.