User: kat

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kat10
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Posts by kat

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Comment: C: Adding wildcards in Snakemake rule
... Okay, thank you for the feedback about the sample names, good point! And re: the original question: I had an issue with incorrect wildcard constraints on the filter argument. Issue solved - thank you again! ...
written 5 months ago by kat10
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Answer: A: Adding wildcards in Snakemake rule
... Thank you for the quick reply! Yes, I have tried that, unsuccessfully. Is there something obvious I'm missing? # List of parameters - move to config file SAMPLES=['T1-XX-2017-1068_S51','L-14-54_S56'] REFS = ['H37Rv'] MAPPERS= ['bowtie2'] FILTERS = ['qfilt','qnoppe'] ...
written 5 months ago by kat10
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Adding wildcards in Snakemake rule
... Hi, I am creating a snakemake pipeline and am having trouble adding an additional wildcard for using different filters. My first rule filters variants and produces two output VCF files, with different filters applied (qfilt or qfiltreg). I would like the second rule to consider {filter} as a wildcar ...
wildcards snakemake written 5 months ago by kat10
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(Closed) Fragment size for Illumina Miseq 2 x 250-bp sequencing
... I am simulating Illumina MiSeq 2 x 250-bp data with ART (https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm) and am wondering the optimal fragment size (mean and st. dev.) for sequencing on this platform. Is there a recommended fragment size or insert size for shearing ...
fragment size illumina miseq sequencing written 18 months ago by kat10
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Answer: A: Comparing VCFs constructed from mapping to different reference genomes
... I am responding to my own question above. I have found a Picard tool `https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_vcf_LiftoverVcf.php` that looks like it would allow me to "lift over" my variants onto another genome build. Thanks! ...
written 18 months ago by kat10
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Comparing VCFs constructed from mapping to different reference genomes
... Hi, I am comparing variant calling pipelines from two authors who have used different versions of a reference genome. Is there a tool that could allow me to compare VCF files constructed from mapping/variant calling on two different ref genomes? Or is there a method for converting the VCF to a VCF f ...
vcf comparisons reference genome written 18 months ago by kat10
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Comment: C: Duplicate SAMSequenceDictionary in SAM file - how to modify SAM header?
... Thank you - yes, remapping, I get the same issue with a duplicated SAM header. This time, I added the -M argument to bwa mem: bwa mem -t 16 -M ${REF_DIR}${ref} ${DATA_DIR}${p1} ${DATA_DIR}${p2} > ${sam} Is this a known issue and is there something I can do to mitigate? Thank you! `@SQ SN:chr1 L ...
written 2.0 years ago by kat10
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Comment: C: Duplicate SAMSequenceDictionary in SAM file - how to modify SAM header?
... Thank you both! I was also running into issues with samtools view -b $sam > test.bam [W::sam_read1] Parse error at line 29991 [main_samview] truncated file. I looked at the parse error lines and the @SQ header is duplicated within my SAM file. Is this a known error with bwa mem? Can I remove al ...
written 2.0 years ago by kat10
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Comment: C: Duplicate SAMSequenceDictionary in SAM file - how to modify SAM header?
... Thanks, yes, the SAM passes samtools quickcheck and unfortunately, samtools reheader only takes input BAM files. ...
written 2.0 years ago by kat10
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Duplicate SAMSequenceDictionary in SAM file - how to modify SAM header?
... Hi, I have used bwa mem to map paired end fastq files to a ref genome and the resulting SAM file has duplicated @SQ lines in the SequenceDictionary: bwa mem -t -M 4 ${REF_DIR}${ref} ${DATA_DIR}${p1} ${DATA_DIR}${p2} > ${sam} The resulting SAM file generates errors using Picard Tools: ...
sam file bwa sequencedictionary written 2.0 years ago by kat10 • updated 2.0 years ago by finswimmer13k

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