User: camerond
camerond • 0
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Posts by camerond
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... Hi finswimmer,
Finally got it working and accepted your answer. Thanks for your help. The final issue I was having was with the zipped dbSNP file. When trying to index with tabix it was throwing an error. Zipping had to be done with bgzip, I'd used something else to zip the file initially.
The fin ...
written 10 weeks ago by
camerond • 0
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... Hi finswimmer,
I have tried your suggestion (pre-update), Alex's and several other methods (including bcftools). The issue I was having with your suggestion is with java. I'd never used Java before, and had issues getting `snpSift` to work.
Tbh I didn't give it a huge amount of time, as I was mor ...
written 10 weeks ago by
camerond • 0
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... Hi Alex,
Thanks for the update. I still can't get this working unfortunately.
I altered my sumstats file using both awk commands, as I'm unsure if the sumstats file is 0 or one based, and ran them separately.
Full header of sumstats pre-awk:
MarkerName Allele1 Allele2 Effect StdErr P.value ...
written 10 weeks ago by
camerond • 0
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... Hi Alex,
Thanks for the response. Just getting round to this now as I was off for Easter.
I had a couple of minor issues with the `sort-bed` command.
Firstly it didn't like the header:
Non-numeric start coordinate. See line 1 in answer.bed.
(remember that chromosome names should not co ...
written 11 weeks ago by
camerond • 0
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... Hi Fin swimmer,
Yes, Allele 1 is always the REF allele.
There are also separate columns for each allele in the sumstats file. The Allele1 column refers to the reference allele and this corresponds the last allele quoted in the MarkerName column (col 1):
MarkerName Allele1 Allele2 Effect StdEr ...
written 12 weeks ago by
camerond • 0
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6 follow
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... I have downloaded a GWAS sumstats file and have a list of SNP locations.
The information for each SNP location is condensed in column 1 of the sumstats file in the following format:
1:100000012_G_T
- 1 = Chromosome
- 100000012 = SNP location
- T = Allele 1
- G = Allele 2
I'm trying to r ...
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... Thanks for your responses. I implemented the second suggestion as it had fewer steps and worked fine, all reads were removed.
I can use that one liner in my pipeline, thanks again.
I'll have a go using the downstream package and see if it likes the header or not. ...
written 3 months ago by
camerond • 0
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... I've wrote this multi-facted question to solve a specific coding problem, but also to bring together information that is covered partially across multiple existing biostars posts that others may find useful.
Part 1 - Edit the bam file
------
I have several bam files that have reads mapped to chro ...
written 3 months ago by
camerond • 0
• updated
3 months ago by
Pierre Lindenbaum ♦ 108k
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