User: nute11a

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nute11a20
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Posts by nute11a

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Comment: C: Filtering BAM file to include PE reads that did not map, even though their mate
... Thank you for your very helpful response. "Do also note that this will not keep alignments for the point of view of the unmapped pairs. Perhaps these are not needed. These would be unmapped alignments where the mate mapped." I'm unclear about this -- I do intend to keep the unmapped mate, if its r ...
written 14 months ago by nute11a20
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Filtering BAM file to include PE reads that did not map, even though their mate did
... Hello! I am trying to filter my BAM file (paired-end read alignment) to 1) Remove pairs that did not map and 2) Contain reads where both reads mapped in their proper pair, and one read mapped but one did not (include the unmapped read if its pair mapped properly) 3) Minimum mapping quality of 10 I ...
filter bam samtools mapping read written 14 months ago by nute11a20 • updated 14 months ago by Istvan Albert ♦♦ 84k
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Comment: A: How to get GQX annotation in vcf file
... Hi Clare, I have a similar question. Were you able to find a solution? ...
written 22 months ago by nute11a20
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Answer: A: Filter heterozygous SNP calls out of a VCF file?
... Hey! I figured it out -- sorry for the late response. I used GATK and did isHet and then set filtered genotypes to no call. Thank you for your help. ...
written 22 months ago by nute11a20
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Filter heterozygous SNP calls out of a VCF file?
... Hello, I was wondering if there was a way to filter out heterozygous SNP calls from a VCF file. I am working with a model that has a doubled haploid genome, so we expect all calls to be homozygous, and any heterozygotes are a false positive which should be removed. Should I be filtering by genotype ...
vcf snp written 23 months ago by nute11a20
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Comment: C: loading plink format (generated by vcftools) file into Haploview
... Hello! I was trying to execute this command using PLINK v1.07 with this command. My file contains only SNPs. plink --file --recode HV --out which returned this: ERROR: Problem parsing the command line arguments. As far as I can tell from the manual, my usage is correct...am I missing something ...
written 2.0 years ago by nute11a20
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Comment: C: In vcf-contrast what do 'NOVELGT', 'NOVELAL' and 'NOVELTY' mean?
... I have the same question. Can anybody help? ...
written 2.1 years ago by nute11a20

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