User: tanya.copley

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tanya.copley10
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Posts by tanya.copley

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Comment: C: replace vcf file ID column
... Ya, I can't figure out why it's doing that. I ended up doing it in R- took forever, but it worked ...
written 3.0 years ago by tanya.copley10
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Comment: C: replace vcf file ID column
... unfortunately this is still giving me the same problem with the two files being on different lines rather than being together on the same line. Thanks though ...
written 3.0 years ago by tanya.copley10
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replace vcf file ID column
... Hi, I am working with two very large vcf files (over 10 Gb each so copy pasting is too large and I want to include the function as part of a script for future studies) and need to replace the "ID" column variables in one of them in order to have matching IDs for merging. First, I removed all rows co ...
vcf phython replace column shell linux written 3.0 years ago by tanya.copley10 • updated 3.0 years ago by Pierre Lindenbaum126k
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Comment: C: GATK removing all primary reads with a secondary alignment
... I am working with soybean, so it does have repetitive regions and is polyploid. My bwa command is as follows: bwa mem -r 1 -a -M -R (RG link) genome input.bam My secondary hits are marked as such (flag 256), but it appears that GATK is not accepting any reads with duplicates. I am also finding th ...
written 3.3 years ago by tanya.copley10
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Comment: C: GATK removing all primary reads with a secondary alignment
... I decided to attempt the HaplotypeCaller instead to see if it would give the same error. Rather, it gave me failing for the MappingQuality. After looking at my bam file, most of my alignments have low MAPQ- mostly 8 or even 0 for primary alignments. I blasted a few sequences in ncbi and ma having ...
written 3.3 years ago by tanya.copley10
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Comment: C: GATK removing all primary reads with a secondary alignment
... So, if I put -rf NotPrimaryAlignment they fail because of this filter even though I have primary alignments for the read. If I put the -filter_bases_not_stored, they fail because of MalformedRead. When I check the headers using picard's ValidateSamFile, I do not get any errors returned. This is w ...
written 3.3 years ago by tanya.copley10
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GATK removing all primary reads with a secondary alignment
... Hi, I am trying to do indel realignment using the GATK tool IndelRealigner. I did my alignment using bwa mem with the -M command for alternative alignments. When I go to use GATK IndelRealigner it removes all of my reads that have the potential to have secondary alignments even if the secondary al ...
gatk bwa indelrealigner written 3.3 years ago by tanya.copley10
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BWA not storing sequence
... Hi, I am having an issue with BWA genome alignment where sequence information is not being stored (i.e. sequence output in bam file is a * ). Can anyone tell me why this is happening and how to retrieve my sequences?? I need them for doing downstream SNP analysis. My code for alignment, sam to bam ...
bwa not storing sequence snp written 3.3 years ago by tanya.copley10 • updated 3.3 years ago by Santosh Anand5.0k
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Platypus callVariants error
... I am continuously getting an error with Platypus, the SNP and variant caller. The install and build appear to have worked properly and I receive no error messages when passing those commands. I get the error after trying to run callVariants: python Platypus.py callVariants --bamFiles=/home/whatsa ...
software error callvariants platypus written 3.3 years ago by tanya.copley10 • updated 3.2 years ago by Biostar ♦♦ 20
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Answer: A: Platypus installation difficulty
... I have the same problem, however the install and build appear to have worked properly. I get the error after trying to run callVariants: python Platypus.py callVariants --bamFiles=/home/whatsaname/script_test/aligned/FC20111007_trimmed_RG_sorted.bam --refFile=/home/whatsaname/gbs/Gmax_ref_genome/G ...
written 3.3 years ago by tanya.copley10

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