vibansal/ancestry

program to estimate admixture coefficients from individual genotype or sequence data

ancestry's Issues

Cannot compile on ubuntu, missing dependencies

There is no Lbsgsb3.0 folder, I've tried finding this exact folder online, but doesn't seem to exist anywhere. Can this be included or a link to that library be included?

Interpretation of results?

Hi,

I have cloned the repo & gone inside of the directory.

However, when I run make or make all I get the following error:

......
/usr/bin/ld: bcftools/libbcf.a(bcfutils.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:44: recipe for target 'samtools' failed
make[1]: *** [samtools] Error 1
make[1]: Leaving directory '/phil/iAdmix/parsebam/samtools-0.1.18'
Makefile:4: recipe for target 'all' failed
make: *** [all] Error 2

Any ideas what the problem may be?

Many thanks in advance, any help would be much appreciated

What is the license for this code?

You mention that you use L-BFGS-B, which is licensed under the "New BSD License", but the terms of that license do not specify application to derivative works. Did you intend to apply this license to your code as well?

Build failing for Ubuntu 21.04

After typing make all, the following output appears:

/usr/bin/ld: hashtable.o:(.bss+0x0): multiple definition of `keypointer'; hapfragments.o:(.bss+0x0): first defined here
/usr/bin/ld: readvariant.o:(.bss+0x0): multiple definition of `keypointer'; hapfragments.o:(.bss+0x0): first defined here
/usr/bin/ld: /tmp/ccLPTRYa.o:DIRECTORY/iadmix/parsebam/hashtable.h:14: multiple definition of `keypointer'; hapfragments.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:8: all] Error 1
make[1]: Leaving directory 'DIRECTORY/iadmix/parsebam'
make: *** [Makefile:5: all] Error 2

The output of lsb_release - a is:

No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 21.04
Release:	21.04
Codename:	hirsute

I don't know about makefiles or ld, but maybe I'm missing some dependency of file?
Thanks in advance

Could you please tag your project.

To promote reproducible science, could you please use git tags. Creating a tag also creates a release for your project. We require tagged releases when building scientific software. Pulling from the master is not reproducible.

I would also recommend using at least a 3 digit semantic versioning scheme; Magor.Minor.Patch. Please do not
follow the git examples by putting a "v" as the leading character. Github will create a "release" when the tag is pushed.

Thank you for making your software available

git tag 1.0.0
git tag push origin 1.0.0

Does this tool involve seeding?

Does this tool involve some kind of random seeding or do you expect it to produce identical results each time it is run with the same input data?

Fatal error while compiling: #include <curses.h>

I got the following error while compiling on a CentOS Linux release 7.5.1804 (Core):

bam_tview.c:5:20: fatal error: curses.h: No such file or directory
#include <curses.h>

I try to figure out how to solve this error which might be useful for other users getting the same error.

where to find allelefreqs for hg38

Hi, I found about ancestry and I would like to know where to find an allelefreqs file for hg38.

The one on DATA is for chr1 only and I presume it's hg19, as it does not find any useful fragments when tested against a hg38 bam.

Any ideas? thanks in advance.

did not find match for chrom: chr1 in hashtable error

Hi again,

I am running ancestry with an hg38 bam file that looks like this:

samtools view -H $bsn | head
@HD     VN:1.5  SO:coordinate
@SQ     SN:chr1 LN:248956422
@SQ     SN:chr2 LN:242193529
@SQ     SN:chr3 LN:198295559
@SQ     SN:chr4 LN:190214555
@SQ     SN:chr5 LN:181538259
@SQ     SN:chr6 LN:170805979
@SQ     SN:chr7 LN:159345973
@SQ     SN:chr8 LN:145138636
@SQ     SN:chr9 LN:138394717

But when I run it with the hg38 .freqs file in DATA/, I am getting this messages:

[...]
reading sorted bamfile /home/ec2-user/data/epi/56001710270833/sample.hg38_merged.deduplicated.bsc.sorted.bam 
did not find match for chrom: chr1 in hashtable 
did not find match for chrom: chr2 in hashtable 
did not find match for chrom: chr3 in hashtable 
processed 2000000 reads, useful fragments 0
did not find match for chrom: chr4 in hashtable 
did not find match for chrom: chr5 in hashtable 
did not find match for chrom: chr6 in hashtable 
did not find match for chrom: chr7 in hashtable 
did not find match for chrom: chr8 in hashtable 
processed 4000000 reads, useful fragments 0

[...]
making input file for ancestry calculations
ancestry admixture calculations for /home/ec2-user/data/epi/56001710270833/sample.hg38_merged.deduplicated.bsc.sorted.bam poolsize is  2
difficult to estimate admixture coefficients with high confidence

final maxval 0.000000 ADMIX_PROP YRI:0.167565 CHB:0.153781 CHD:0.016052 TSI:0.197848 MKK:0.013955 LWK:0.053050 CEU:0.203604 JPT:0.194147 
YRI:0.1676:0.00 CHB:0.1538:0.00 CHD:0.0161:0.00 TSI:0.1978:0.00 MKK:0.0140:0.00 LWK:0.0530:0.00 CEU:0.2036:0.00 JPT:0.1941:0.00 FINAL_ALL_PROPS
YRI:0.1676:0.00 CHB:0.1538:0.00 CHD:0.0161:0.00 TSI:0.1978:0.00 MKK:0.0140:0.00 LWK:0.0530:0.00 CEU:0.2036:0.00 JPT:0.1941:0.00 FINAL_NZ_PROPS bins 200 ssq 0.000000
LL 0.000000 LL_exp 0.000000 0.000000 -nan

Any ideas what the issue might be? Thanks in advance.

most complete allele frequency file possible with public data?

Hi,

I would like to generate the most complete allele frequency file possible with public data for hg38, so that I can feed that into the ancestry tool for each of my bam files.
What is the most complete allele frequency file that can be built nowadays with public data? E.g. would it be from the latest release of the 1000g project or is it possible to find a more complete file, which more representative populations, from other projects?

Thanks in advance.