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Looks like something changed between 1.1 and 1.3 regarding the -T -o options to sort. See the log file below.
```
### samtools faidx reference/ref.fa
### bwa index reference/ref.fa
[bwa_index] Pac…
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Hi, I was trying to use fastQValidator with **gzipped** fastq files, but I am getting an error, see below. In the manual I read "Consumes gzipped and uncompressed text files transparently". Can you cl…
dastu updated
8 years ago
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Not sure what's going on here.. see error msg below. The error seems to be `bam readcount < fastq readcount`.
For info: the bam file is based on Haloplex, i.e. an amplicon strategy. Coverage in the…
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Would you guys be open to gzipping the output fastq files at the end of the pipeline? And converting sam to sorted bam, in the interest of compression.
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Hi,
I tried to run CollectMultipleMetrics and provide a target region file. But with or without the target region as input, the outputs are same.
I tried to add BAM file header to the target region…
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When there is a bgzipped vcf we should use cython for parsing, but still allow unzipped vcf files.
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Hello,
I'm running Picard's MarkDuplicates tool on my paired-end exome sequencing data. The tool is definitely removing duplicate reads (1-4% of the library total), but it is having trouble with read…
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Try to run the test (test_snv_bwamem.sh), resulting following error message:
Command:
../test/test_snv_bwamem.sh 1 1 /net/kodiak/volumes/river/shared/users/ltfang/link_to_reference/human_g1k_v37_deco…
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bowtie2 can align fastq files that are gzipped. If the full fastq files are not needed elsewhere in the miseqpipeline, we can symlink the gzipped fastq files to the working directory of the miseqpipe…
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Need to support gzip input files
- Both .fastq.gz and .sff.gz