Invalid option `-p'

[npsonis]

Hi again,

I am running pileupCaller with -p POP enabled but I get the following error

Invalid option `-p'
Did you mean one of these?
-h
-d
-f
-e

The same if I use: --plinkOut POP

It works with -e. If neither is used I get: Missing: (-e|--eigenstratOut <FILE_PREFIX>)

Perhaps -p is not implemented yet?

Version: 1.5.1

[stschiff]

Hmm, that's odd. Are you sure you're using the option correctly? It expects a filename as argument, like -p my_plink_file_prefix. You can check the online help using pileupCaller --help. Have I perhaps made a mistake in the documentation somewhere?

[npsonis]

Yes my filename is POP. It works with -e POP.

[stschiff]

Could you please post here the output of pileupCaller --help?

[npsonis]

Usage: pileupCaller [--version]
(--randomHaploid | --majorityCall [--downSampling] |
--randomDiploid) [--keepIncongruentReads]
[--seed <RANDOM_SEED>] [-d|--minDepth ]
[--skipTransitions | --transitionsMissing |
--singleStrandMode] (-f|--snpFile )
[(-e|--eigenstratOut <FILE_PREFIX>) [--samplePopName POP] |
(-p|--plinkOut <FILE_PREFIX>) [--samplePopName POP]]
(--sampleNames NAME1,NAME2,... | --sampleNameFile )
PileupCaller is a tool to create genotype calls from bam files using
read-sampling methods. To use this tool, you need to convert bam files into
the mpileup-format, specified at http://www.htslib.org/doc/samtools.html
(under "mpileup"). The recommended command line to create a multi-sample
mpileup file to be processed with pileupCaller is

  samtools mpileup -B -q30 -Q30 -l <BED_FILE> -R -f <FASTA_REFERENCE_FILE>
      Sample1.bam Sample2.bam Sample3.bam | pileupCaller ...

You can lookup what these options do in the samtools documentation. Note that
flag -B in samtools is very important to reduce reference bias in low coverage
data.

This tool is part of sequenceTools version 1.5.1

Available options:
--version Print version and exit
-h,--help Show this help text
--randomHaploid This method samples one read at random at each site,
and uses the allele on that read as the one for the
actual genotype. This results in a haploid call
--majorityCall Pick the allele supported by the most reads at a
site. If an equal numbers of alleles fulfil this,
pick one at random. This results in a haploid call.
See --downSampling for best practices for calling
rare variants
--downSampling When this switch is given, the MajorityCalling mode
will downsample from the total number of reads a
number of reads (without replacement) equal to the
--minDepth given. This mitigates reference bias in
the MajorityCalling model, which increases with
higher coverage. The recommendation for rare-allele
calling is --majorityCall --downsampling --minDepth 3
--randomDiploid Sample two reads at random (without replacement) at
each site and represent the individual by a diploid
genotype constructed from those two random picks.
This will always assign missing data to positions
where only one read is present, even if minDepth=1.
The main use case for this option is for estimating
mean heterozygosity across sites.
--keepIncongruentReads By default, pileupCaller now removes reads with
tri-allelic alleles that are neither of the two
alleles specified in the SNP file. To keep those
reads for sampling, set this flag. With this option
given, if the sampled read has a tri-allelic allele
that is neither of the two given alleles in the SNP
file, a missing genotype is generated. IMPORTANT
NOTE: The default behaviour has changed in
pileupCaller version 1.4.0. If you want to emulate
the previous behaviour, use this flag. I recommend
now to NOT set this flag and use the new behaviour.
--seed <RANDOM_SEED> random seed used for the random number generator. If
not given, use system clock to seed the random number
generator.
-d,--minDepth specify the minimum depth for a call. For sites with
fewer reads than this number, declare
Missing (default: 1)
--skipTransitions skip transition SNPs entirely in the output,
resulting in a dataset with fewer sites.
--transitionsMissing mark transitions as missing in the output, but do
output the sites.
--singleStrandMode [THIS IS CURRENTLY AN EXPERIMENTAL FEATURE]. At C/T
polymorphisms, ignore reads aligning to the forward
strand. At G/A polymorphisms, ignore reads aligning
to the reverse strand. This should remove post-mortem
damage in ancient DNA libraries prepared with the
non-UDG single-stranded protocol.
-f,--snpFile an Eigenstrat-formatted SNP list file for the
positions and alleles to call. All positions in the
SNP file will be output, adding missing data where
there is no data. Note that pileupCaller
automatically checks whether alleles in the SNP file
are flipped with respect to the human reference, and
in those cases flips the genotypes accordingly. But
it assumes that the strand-orientation of the SNPs
given in the SNP list is the one in the reference
genome used in the BAM file underlying the pileup
input. Note that both the SNP file and the incoming
pileup data have to be ordered by chromosome and
position, and this is checked. The chromosome order
in humans is 1-22,X,Y,MT. Chromosome can generally
begin with "chr". In case of non-human data with
different chromosome names, you should convert all
names to numbers. They will always considered to be
numerically ordered, even beyond 22. Finally, I note
that for internally, X is converted to 23, Y to 24
and MT to 90. This is the most widely used encoding
in Eigenstrat databases for human data, so using a
SNP file with that encoding will automatically be
correctly aligned to pileup data with actual
chromosome names X, Y and MT (or chrX, chrY and
chrMT, respectively).
-e,--eigenstratOut <FILE_PREFIX>
Set Eigenstrat as output format. Specify the
filenames for the EigenStrat SNP, IND and GENO file
outputs: <FILE_PREFIX>.snp, <FILE_PREFIX>.ind and
<FILE_PREFIX>.geno. If not set, output will be
FreqSum (Default). Note that freqSum format,
described at
https://rarecoal-docs.readthedocs.io/en/latest/rarecoal-tools.html#vcf2freqsum,
is useful for testing your pipeline, since it's
output to standard out
--samplePopName POP specify the population name of the samples, which is
included in the output *.ind.txt file in Eigenstrat
output. This will be ignored if the output format is
not Eigenstrat (default: "Unknown")
-p,--plinkOut <FILE_PREFIX>
Set Plink as output format. Specify the filenames for
the Plink BIM, FAM and BED file outputs:
<FILE_PREFIX>.bim, <FILE_PREFIX>.fam and
<FILE_PREFIX>.bed. If not set, output will be FreqSum
(Default). Note that freqSum format, described at
https://rarecoal-docs.readthedocs.io/en/latest/rarecoal-tools.html#vcf2freqsum,
is useful for testing your pipeline, since it's
output to standard out
--samplePopName POP specify the population name of the samples, which is
included in the output *.ind.txt file in Eigenstrat
output. This will be ignored if the output format is
not Eigenstrat (default: "Unknown")
--sampleNames NAME1,NAME2,...
give the names of the samples as comma-separated list
(no spaces)
--sampleNameFile give the names of the samples in a file with one name
per line

My command that works is the folowing (does not work with -p instead of -e):
pileupCaller --randomHaploid --sampleNameFile Kinship_IDs.txt --samplePopName POP -e POP -f 1240K.snp < 1240K.pileup

[stschiff]

OK, the issue is that the -e flag means --eigenstratOut, while the -p flag means --plinkOut. You can't have both of these at the same time. When you try without the -e POP flag this command above should work.

The following command should work with the testData provided in the repository:

cd test/testDat
pileupCaller --sampleNames 12880A,12881A,12883A,12885A --randomHaploid --singleStrandMode -f 1240k_eigenstrat_snp_short.snp.txt -p testOut < AncientBritish.short.pileup.txt

[npsonis]

Sorry for reopened the thread, but the problem remains.
This works:
pileupCaller --randomHaploid --sampleNameFile Kinship_IDs.txt --samplePopName POP -e POP -f 1240K.snp < 1240K.pileup
This doesn't:
pileupCaller --randomHaploid --sampleNameFile Kinship_IDs.txt --samplePopName POP -p POP -f 1240K.snp < 1240K.pileup

I copied the command and just changed the letter e to p, to make sure that no typing error exists.

The error remains the same as I wrote previously:
Invalid option `-p'
Did you mean one of these?
-h
-d
-f
-e

However, this does works properly, as you propose:
cd test/testDat
pileupCaller --sampleNames 12880A,12881A,12883A,12885A --randomHaploid --singleStrandMode -f 1240k_eigenstrat_snp_short.snp.txt -p testOut < AncientBritish.short.pileup.txt

EDIT!!!
I just figure out that if I change the order of the arguments it works:
pileupCaller --randomHaploid --sampleNameFile Kinship_IDs.txt -p POP -f 1240K.snp --samplePopName POP < 1240K.pileup

So, the problem is with --samplePopName preceding -p.

[stschiff]

Yes, I understand now. Indeed, there is an implied order in these arguments, because --samplePopName makes only sense with either -p or -e set. I agree this is a bit weird and intransparent. I can easily fix that. I reopen this issue to remind myself.

[stschiff]

This is fixed in v1.5.2