User: LTDavid

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LTDavid20
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20
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New User
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Website:
https://takir.org/
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8 months, 4 weeks ago
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1 year, 4 months ago
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c******@takir.org

Posts by LTDavid

<prev • 11 results • page 1 of 2 • next >
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IndexError: list index out of range with relatedness_v1.py
... I'm running python code `relatedness_v1.py` which takes as input an IBD file and produces a relatedness matrix. When I run the code, I get an IndexError that I don't understand how to fix. To get the relatedness_v1.py code, visit this link [http://faculty.washington.edu/sguy/ibd_relatedness.html][1] ...
python relatedness_v1 index error written 14 months ago by LTDavid20 • updated 11 weeks ago by larryhems0
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Answer: A: convert ancestry.com text file to vcf
... I decided to try to convert the ancestry.com txt file to a 23andMe formatted txt file, which may could then be used in the existing bcftools convert command. I got it to work up to converting the format from ancestry.com to 23andMe using this: 7z x SampleFile.zip ; mv AncestryDNA.txt SampleFile ...
written 14 months ago by LTDavid20
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convert ancestry.com text file to vcf
... How do you convert a text file from Ancestry.com to vcf format? I understand that I could convert from 23andMe to vcf with something like: bcftools convert -c ID,CHROM,POS,AA -s SampleFile -f reference/Homo_sapiens.GRCh37.dna.primary_assembly.fa --tsv2vcf Data/SampleFile/AncestryDNA.txt -Oz -o ...
vcf ancestry.com ancestrydna convert written 14 months ago by LTDavid20 • updated 3 months ago by maribuon0
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Comment: C: "ERROR:...Base position exceeds Integer.MAX_VALUE" using Refined IBD with map fi
... No, I don't think I have base positions larger than that. My last line in my map file is this: X . 180.837755 155699751 In the Refined IBD output, the following shows up: Window 110 (X:37291432-93947399) Then the error message posted in my original question followed by: terminating ...
written 16 months ago by LTDavid20
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"ERROR:...Base position exceeds Integer.MAX_VALUE" using Refined IBD with map file
... When using Refined IBD with a PLINK map file, I received the following error: ERROR: java.lang.IllegalArgumentException: Base position exceeds Integer.MAX_VALUE Are all genetic distances in cM units (in command line and in genetic map)? java.lang.IllegalArgumentException: Base positio ...
beagle map refined-ibd plink written 16 months ago by LTDavid20 • updated 16 months ago by Philipp Bayer6.8k
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Comment: C: convert GRCh38 FASTA .fa to .vcf
... Thank you very much, Ahill. The NCBI dbSNP database is exactly what I needed. They even provide the latest release already in both VCF and JSON formats on their [About Reference SNP (rs)][1] page. I greatly appreciate you asking me more details about why I was asking my question and investigating my ...
written 16 months ago by LTDavid20
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Comment: C: BEAGLE 4.0 with ped file output into Refined IBD not identifying segments proper
... I used plantimals/2vcf to convert from AncestryDNA zip files to vcf files. Some of the markers didn't transfer over to the output file. Those that did are correct. 2vcf uses GRCh37 as reference.vcf file. ...
written 16 months ago by LTDavid20
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Comment: C: convert GRCh38 FASTA .fa to .vcf
... I'm trying to take raw DNA files downloaded from AncestryDNA and 23andMe and determine relatedness among the sample. I'm using plantimals/2vcf to convert from (txt)zip to vcf.gz. The problem is that there are markers missing in the vcf file that were in the zip file. For example, in my zip file down ...
written 16 months ago by LTDavid20
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convert GRCh38 FASTA .fa to .vcf
... How do you convert the GRCh38.fa FASTA file to a VCF file? The file is from Ensembl primary_assembly [ ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/][1] [1]: ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/ ...
fasta vcf written 16 months ago by LTDavid20 • updated 16 months ago by Ahill1.9k
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How do I convert GrCh37 text files to a map file?
... How do I go from the multiple GrCh37 text files separated by chromosome to a single map file that I can use in IBD estimation? I have the following information about the map argument: map=[*file*] specifies a [PLINK][1] format genetic map with cM units. HapMap GrCh36 and GrCh37 genetic maps in PLIN ...
map ibd written 16 months ago by LTDavid20

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