WebDec 1, 2014 · The purpose of the -T option is if you have a BAM file that doesn't have a header for some reason. Then you can replace it with the information from an indexed fasta file (hopefully the reads were aligned to that fasta file...otherwise the alignments will be to the wrong chromosomes). Web1 Answer. The cause of the error is that your input file is truncated or /tmp is running out of space. If you can do samtools view -H input.bam without error (reading the header also …
[Samtools-help] samTools on solaris 10: samtools view [main
WebSAMtools sort has been unable to parse its input, which it thought was SAM (mostly because it couldn't be recognised as another format e.g. BAM). This is because sed 's/^/LP1-/' is putting LP1- at the front of every line. If the output of samtools fixmate is SAM, then this LP1 is garbling the SAM header lines. Web[main_samview] fail to read the header from "Input.rep1.sam". I'm currently using the bismark converted genome as my reference genome , and my command line : `ls *.fq.gz cut -d '.' -f 1 while read id; do ... And of course cannot run the `samtools view -H` But this would work with my paried end sample 😭 t5 and t5008
samtools-reheader(1) manual page
WebAug 3, 2024 · The samtools error is likely because it is receiving no output from the bwa mem command. Try running the bwa mem command by itself, and see if it returns a … WebI.e. samtools view? If the header's bad, might be possible to figure out what's wrong with it (missing, corrupted, something else) by just looking at it with samtools view -H. 1 kellogg76 • 4 yr. ago samtools view -H filename.bam gives the same error as before. WebThe file was converted from sam to bam using the following command: samtools view -bS sample.sam > sample.bam. [E::bgzf_read] bgzf_read_block error -1 after 194938 of … t5 arachnid\u0027s