[Scorpion43]

Thank you Cytosine, that did it !!!

I had tried adding those two parameters from another thread I had seen before I registered with SEQanswers, (but not the same thread that you have directed me to).

As I said before, when something does not work I tend to remove it again rather that clog up a file with apparently non-working parts.

This is what I now get:-

$ ./samtools.exe

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd

Usage: samtools <command> [options]

Command: view SAM<->BAM conversion
sort sort alignment file
mpileup multi-way pileup
depth compute the depth
faidx index/extract FASTA
index index alignment
idxstats BAM index stats (r595 or later)
fixmate fix mate information
flagstat simple stats
calmd recalculate MD/NM tags and '=' bases
merge merge sorted alignments
rmdup remove PCR duplicates
reheader replace BAM header
cat concatenate BAMs
bedcov read depth per BED region
targetcut cut fosmid regions (for fosmid pool only)
phase phase heterozygotes
bamshuf shuffle and group alignments by name

Thank you so much for leading me by the hand ... now I might be able to get on with my DNA analysis of my BAM files.

Cheers
Dennis Wright

https://www.irishtype3dna.org/

[BurlEarl]

Hi all,

From my experience Cygwin will be a continuous pain in the rear when trying to get new programs to compile. Unless this is really the only thing you can imagine having to compile, I would recommend buying another HD and installing a linux distribution. Because Cygwin is light weight, it is missing a ton of standard libraries. Since a lot of programs have dependencies that are met with standard Linux distros they are just not listed. What ended up happening for me was i tried $ make, found the compiler complaint, then installed Cygwin library and rinse and repeat for many iterations.

One pretty good newbie solution/stepping stone is Bio-Linux, which is based on Ubuntu (the window user friendly Linux distro). It comes with a ton of useful software preinstalled along with all their dependencies (obviously). These same packages are used for a ton of programs, so in the end much less time sifting through $ make outputs all day
It has been well worth the investment in the linux learning curve.

Bio-linux site:

http://environmentalomics.org/bio-linux/

[Scorpion43]

Thank you BurlEarl for your suggestion but I have no need, or desire to dive in deeper into Unix/Linux.

I taught myself Microsoft Basic in 1980 and have had a computer at home since then. At that time I taught myself and wrote programs in Z80 machine language. But I have not had a need to learn C+, C++, Perl, Ruby or any of the other languages. In recent times I have confined myself to HTML and CSS to build and maintain my website and at 70 can't be bothered in learning more that I have to!

While I haven't bothered to work out the intricacies of PATHs, SOURCEs and ENVIRONMENTs I am now able to drop a .bam file into the Samtools-0.1.19 folder, open the Cygwin Terminal window, cd to /samtools-0.1.19 directory and on issuing the command:-
./samtools.exe index xxxx.bam
after a short delay, the xxxx.bam.bai index file appears in the samtools-0.1.19 directory.

I can then use IGV 2.3.34 (Intergrative Genomics Viewer) to analyse the DNA results emanating from Next Generation Sequencing of the Y Chromosome.

That was all I needed Samtools to do for me so thanks to SEQanswers for assisting me to that end.

[BurlEarl]

Well you are certainly more qualified than me! I just started this bioinformatics journey (hence all the newbie info). Glad it's working for you. Good luck with analysis and whatnot.

Earl

[Jeremy]

A more functional alternative to cygwin would be bio-linux (ubuntu with many programs such as samtools pre installed) in a virtual box.