User: kstafford32

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Posts by kstafford32

<prev • 13 results • page 1 of 2 • next >
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Comment: C: could not load index bfc tools af-dis plugin
... Thank you, I index it using `bcftools index`, but still used the vcf.gz for the script and it worked. Still learning what these types of files mean, and how the script uses these various types of files. Appreciate your help! ...
written 6 days ago by kstafford320
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Comment: C: could not load index bfc tools af-dis plugin
... I actually did index the af.vcf.gz file upon downloading it from the site.... I also tried to index it again and it said that I already have done so. I don't think this indexing instruction applies to my data file...? ...
written 6 days ago by kstafford320
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Comment: C: could not load index bfc tools af-dis plugin
... Index to make it a tbi file? Then should I use the tbi files for this af-dist script? Thanks ...
written 6 days ago by kstafford320
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could not load index bfc tools af-dis plugin
... Hello, I am attempting to use the af-dist bcftools plugin to detect potential strand issues using the instructions found here: https://samtools.github.io/bcftools/howtos/plugin.af-dist.html My script: bcftools annotate -c INFO/AF -a af.vcf.gz DAC14_chr1_hg38_nonduplicates_fix.vcf.gz | bcftoo ...
vcf bcf tools af-dist imputation written 6 days ago by kstafford320
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Comment: C: bcf tools fixref error
... Yes, you're right. So that any other rookies don't make this mistake, use: wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta ^ This one worked for some reason... ...
written 6 days ago by kstafford320
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Comment: C: bcf tools fixref error
... interesting.... perhaps I downloaded it incorrectly? head -n 3 /sc/arion/projects/psychgen2/MAP2_dac/data/imputation/DAC14_send_to_topmed/Homo_sapiens_assembly38_withchr.fasta I used this to download...perhaps cannot do this from a cloud? wget https://storage.cloud.google ...
written 6 days ago by kstafford320
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bcf tools fixref error
... Hello, I am trying to run the fixref plugin found here, to correct for snpflip errors in my topmed imputation. I found this code here: https://samtools.github.io/bcftools/howtos/plugin.fixref.html for i in {1..22} do bcftools norm --check-ref e -f $OUTDIR/DAC14_send_to_topmed/Homo_sapie ...
fixref bcftools imputation snpflip topmed written 7 days ago by kstafford320
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Beagle conform-gt error
... Hi, I ran a beagle conform-gt script to fix my snpflip topmed qc imputation error. Conform-gt gave this error as well as many other similar ones for different chromosomes: Exception in thread "main" java.lang.IllegalArgumentException: Duplicate marker [OUTDIR/conformgt_HG38_Ref_2/ALL.chr1 ...
conformgt java imputation tomped beagle written 10 days ago by kstafford320
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Comment: C: Beagle Conform-gt Java Error
... It worked. Thank you greatly. I spent hours "googling" what "duplicate arguments ref at..." meant. Makes sense now. Thank you so much! ...
written 11 days ago by kstafford320
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Comment: C: Beagle Conform-gt Java Error
... Not entirely sure what you're asking. But no, other than using these wget codes, I used my `for` as is: wget http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/sample_info/integrated_call_samples_v3.20130502.ALL.panel wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/rele ...
written 11 days ago by kstafford320

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