Comments (3)
could you expand on the first point? you mean you want to avoid argument list too long
error or something?
for the 2nd point, indexcov only does within sample normalization, not between sample. I did have a mode where you could specify that the first $N samples were of interest and the remaining were background--to give an idea of how a maybe small $N looks given a large background, but I removed this as it made the code and interface more complex. I'm hesitant to revisit, but I might be convinced.
from goleft.
? you mean you want to avoid argument list too long error or something?
yes. Something like what the broad is doing with the '.list' suffix: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_engine_CommandLineGATK.php#--input_file
An input file containing sequence data mapped to a reference, in BAM or CRAM format, or a text file containing a list of input files (with extension .list).
I'm hesitant to revisit, but I might be convinced
I wouldn't be able to convince you. I wondered if there was something to explore here.
from goleft.
? you mean you want to avoid argument list too long error or something?
yes. Something like what the broad is doing with the '.list' suffix: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_engine_CommandLineGATK.php#--input_file
that's doable, though I suspect if your command is that long then it'll be hard to do
much with the output. Though I guess you have your own viewer that can overcome the limitations of the
html one included. Let's keep this open and I'll try to get around to adding that.
An input file containing sequence data mapped to a reference, in BAM or CRAM format, or a text file containing a list of input files (with extension .list).
I'm hesitant to revisit, but I might be convinced
I wouldn't be able to convince you. I wondered if there was something to explore here.
There may be, but I don't have the bandwidth for now.
from goleft.
Related Issues (20)
- indexcov support for csi indexes HOT 2
- ndexcv: excluding chromosome: NC_031965 because of exclude-pattern: ^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d HOT 2
- goleft_linux64 covstats error: panic: EOF HOT 7
- coverage of the customized genome HOT 2
- error: bam is required HOT 4
- link to golang typo
- suggestion: zoomable chromosome depth plots in indexcov HOT 1
- indexcov shows stepwise coverage distribution HOT 4
- Feature request: New option --exclude for covstats HOT 2
- Indexcov errors HOT 2
- error on depth, seems to make temp file it can't find
- Negative alnSpan error HOT 2
- No longer possible to build from source or include in a Docker image HOT 2
- Running Indexcov on cram files with different paths HOT 2
- What is the value of the insert size ? HOT 2
- indexcov: usage with long reads ? HOT 1
- Indexcov searching for cram.bai HOT 1
- covstats: % unmapped calculation seems inaccurate (>3000%, etc) HOT 5
- indexcov everything is DEL or DUP HOT 2
- Release Linux aarch64 binary HOT 4
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from goleft.