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
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
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