WebFeb 19, 2024 · The text was updated successfully, but these errors were encountered: WebJun 17, 2024 · The most common samtools view filtering options are: -q N – only report alignment records with mapping quality of at least N ( >= N ). -f 0xXX – only report alignment records where the specified flags are all set (are all 1) you can provide the flags in decimal, or as here as hexadecimal. -F 0xXX – only report alignment records where the ...
samtools view: writing to standard output failed: Broken pipe
WebMar 23, 2024 · The problem is that without an input file, samtools sort tries to read from stdin. Using a recent samtools, you can however coordinate sort the SAM and write a … http://www.htslib.org/doc/samtools-reheader.html thomas josef schmitz
samtools sort [bam_merge_core] [bam_sort_core] errors?
WebJun 7, 2011 · Try truncating the file to see if it's a filesystem issue (assuming it's a 64-bit system?): head -100000 outX300.sam > test100k.sam samtools view -bS -o test100k.bam test100k.sam 2. Try simply moving the file elsewhere and trying again? 3. Try Version: 0.1.7 ? WebMar 23, 2024 · The problem is that without an input file, samtools sort tries to read from stdin. Using a recent samtools, you can however coordinate sort the SAM and write a sorted BAM using: samtools sort -o "$ {baseName}.bam" "mapped_$ {baseName}.sam" WebJul 8, 2024 · Update: it's good to know that the samtools / bcftools pipelines are at least producing consistent results, which suggests that the error is not associated with the output format on the mpileup side of the pipeline, and also good to see that you've identified that this was a memory issue. uhaul moundsville wv