User: Molly_K

gravatar for Molly_K
Molly_K40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 months, 1 week ago
Joined:
4 years, 6 months ago
Email:
k******@gmail.com

Posts by Molly_K

<prev • 14 results • page 1 of 2 • next >
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Comment: C: bcftools filtering INFO column issues (empty output)
... Hi Pierre, I used the following command line and noticed a drop in the row numbers > bcftools view -e '(R2<0 || R2>=0)' $FILE/chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz > test1.vcf wc -l chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz 1176573 chr22_rsq_filtered.vcf_remov ...
written 3 months ago by Molly_K40
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Comment: C: bcftools filtering INFO column issues (empty output)
... I apologize for the weird behaviour of the file. I think after copy paste from the terminal there are some tabs missing. Here's a link to the first 100 rows of the vcf file that I extracted bcftools view $FILE/chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz | head -100 > $FILE/test2.vcf h ...
written 3 months ago by Molly_K40
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Comment: C: bcftools filtering INFO column issues (empty output)
... Updated the original post to fit in the first 19 rows. It's the header + the first snp. If I don't limit the row number, it would keep running till the end of the file. Thanks. ...
written 3 months ago by Molly_K40
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Comment: C: bcftools filtering INFO column issues (empty output)
... Hi Pierre, here's the output [filter.c:2278 filters_init1] Error: the tag "GQ_MEAN" is not defined in the VCF header ...
written 3 months ago by Molly_K40
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bcftools filtering INFO column issues (empty output)
... How can I filter out variants with R2!="." in the INFO column? > bcftools view -i 'INFO/R2!="."' -Oz $FILE -o $OUTFILTERED The above generated a vcf.gz file with only the header. I have used the same command line to filter VCF file based on the R2 score and it worked fine. Just wondering what ...
vcf filter bcftools missing info written 3 months ago by Molly_K40
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Comment: C: Genotype input in matrix eqtl with dosage dataset
... This is highly inappropriate. Thanks but no thank. ...
written 4 months ago by Molly_K40
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Genotype input in matrix eqtl with dosage dataset
... I have performed eQTL with matrix eQTL tool before with hard call genotype. I wonder if anyone has tried with dosage genotype. The data format is SNP A1 A2 F1 I1 F2 I2 F3 I3 rs0001 A C 0.98 0.02 1.00 0.00 0.00 0.01 rs0002 G A 0.00 1.00 ...
dosage genotype eqtl written 4 months ago by Molly_K40 • updated 4 months ago by devidjohn470
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Comment: C: michigan imputation server
... Hi Teresa, I am interested in if you have found a way to solve the problem with the dosage data. I wonder what did you do with your DosageConvertor output file? How did you QC on that? Thanks! ...
written 4 months ago by Molly_K40
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Answer: A: how to unzip Michigan imputation server output compressed folder
... The imputation server encrypts all zip files by default using the 256-bit key. The standard unzip program does not work, you will need to install 7-Zip program. Once you have the program, type in the following: 7z e file.zip Then enter your password. ...
written 4 months ago by Molly_K40
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Comment: C: vcftools: unwanted filtering
... I basically realized it's a misunderstanding on my end so I deleted the question, realizing it isn't even a good question, but if someone has the same doubt when interpreting the results, this post may be helpful :P ...
written 12 months ago by Molly_K40

Latest awards to Molly_K

Scholar 12 months ago, created an answer that has been accepted. For C: vcftools: unwanted filtering
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Permutation using Plink

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