User: jsneaththompson

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Posts by jsneaththompson

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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... Connor is using pysam 0.7.5 ...
written 11 days ago by jsneaththompson0
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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... Ah, fair enough. Yes I know some python. ...
written 11 days ago by jsneaththompson0
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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... I managed to switch to pysam 0.8.4 with pip, but I'm still getting the same error message when I try to run Connor ...
written 11 days ago by jsneaththompson0
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Comment: C: Connor Deduplication - AttributeError: 'module' object has no attribute 'Alignme
... According to pip, I'm using v 0.11.2.2 Connor says it requires pysam>=0.8.4,<0.9.1, how would I go about changing the pysam version? ...
written 11 days ago by jsneaththompson0
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Connor Deduplication - AttributeError: 'module' object has no attribute 'AlignmentFile'
... I'm attempting to use [Connor][1] to deduplicate some bam files in my variant calling pipeline, but so far whenever I attempt to run Connor I get the following error message: 2017-07-17 10:32:28|ERROR|An unexpected error occurred 2017-07-17 10:32:28|ERROR|Traceback (most recent call last): ...
barcoding alignment deduplication connor written 11 days ago by jsneaththompson0
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Comment: C: Pindel and GATK AD Concordance
... Thanks for the advice! ...
written 7 weeks ago by jsneaththompson0
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Pindel and GATK AD Concordance
... was hoping to get some advice on working with the AD field for variants in VCFs produced by Pindel and Pindel2VCF. My lab has a variant calling pipeline that uses GATK's UnifiedGenotyper for calling SNVs and small Indels, as well as using Pindel to call deletions and short insertions. As part of o ...
variant calling gatk allele depth pindel written 7 weeks ago by jsneaththompson0 • updated 7 weeks ago by Dan Gaston6.8k
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Depth of coverage in Bam file does not match depth in VCF file
... My lab has a variant calling pipeline where sorted bam files are used as input for Pindel. The pindel output files (D and SI) are then converted to vcfs for annotation. However, when the sorted bam files are loaded into IGV the loaded coverage file gives one value for depth at a variant's location ...
indel variant calling pindel coverage igv written 11 weeks ago by jsneaththompson0 • updated 11 weeks ago by tangming20052.1k

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