WebJun 17, 2024 · For that we need to count the total number of mapped reads. Here we can just use the -c ( c ount only) option to samtools view. Count all mapped reads samtools view -c -F 0x4 yeast_pe.sort.bam There should be 547664 mapped alignments. Knowing these two numbers we can just divide them, using awk (remember, bash only does integer … WebApr 8, 2013 · -bash-3.2$ samtools sort x.bam x.sorted [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_sort_core] truncated file. Continue anyway. Segmentation fault Samtools was used to generate the bam files so it's strange that it can't recognize a file that it's generated itself.

"samtools: no @sq lines in the header" - metagenome!

WebI am running samtools 1.3.1 I have ~ 1.5 mil singleton and ~ 100 mil paired end reads from each sample (the singletons are when one of the pair failed QC). For the singleton alignments, I was able to use Samtools to sort, index, filter, index again and calculate coverage relative to my .bed file. However, I can not sort my paired-end read ... WebNov 20, 2013 · One can ask the view command to report solely the header by using the -H option. samtools view -H sample.sorted.bam Capture the FLAG. As we discussed earlier, … tequila hotel guadalajara

samtools/samtools-stats – BioLib

WebMay 25, 2024 · mdehoon commented on May 25, 2024. That's because samtools now rejects completely empty files, on the assumption that they were made by an upstream process that failed rather than deliberately. … http://www.htslib.org/doc/samtools-ampliconstats.html WebOct 2, 2024 · using samjdk and invoking the function getReadGroup () getReadGroup () returns The SAMReadGroupRecord from the SAMFileHeader for this SAMRecord, or null if 1) this record has no RG tag, or 2) the header doesn't contain the read group with the given ID.or 3) this record has no SAMFileHeader tequila hawaiian punch