Tag: EOF

Problem with using flagstat after bowtie2 alignment

I’m running bowtie2 to align multiple samples to one reference genome, and then run samtools flagstats to output the results. All but two samples have aligned and I’ve managed to run flagstat on them. For those two samples, when I run flagstat, I first get: [W::bam_hdr_read] EOF marker is absent….

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Alternative to samtools quickcheck with bash scripting

Alternative to samtools quickcheck with bash scripting 1 Is there an alternative to samtools quickcheck? I need to perform a check some bam files in order to verify that they’re not truncated. Nevertheless, I can’t use samtools since in the linux machine where I have the data I can’t install…

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bamdst gives error “EOF marker is absent. The input is probably truncated.”

bamdst gives error “EOF marker is absent. The input is probably truncated.” 0 I created a set of bam files from Poolseq data using bwa -aln, and all of the output files gave the following error when I ran bamdst to get summary statistics on read depth: “EOF marker is…

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samtools mpileup fail to create bcf

samtools mpileup fail to create bcf 1 I have indexed my reference.fasta using bowtie2: bowtie2-build reference.fasta reference.fasta created the bam file form the sam file using samtools, sorted and indexed the bam file: samtools view -S -b Sample1_mapped.sam > Sample1_mapped.bam samtools sort Sample1_mapped.bam -o Sample1_sorted > Sample1_sorted.bam samtools index Sample1_sorted.bam…

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split pdb into submodels

split pdb into submodels 1 There is a program called pdbsplitchains in this repository: github.com/ACRMGroup/bioptools pdbset from the CCP4 package can do all kinds of manipulations on PDB files – including splitting by chain – but it requires a bit of scripting. For example, these several lines would extract chain…

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EOF marker absent in VCF

EOF marker absent in VCF – can this be safely ignored? 0 Hi, I generated a VCF file using a bcftools mpileup | bcftools call pipeline. I have done this before, and the file produced then looks fine. However, the log for this one had [W::bgzf_read_block] EOF marker is absent….

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Error while subsetting VCF – error doesn’t check out with (z)grep

Error while subsetting VCF – error doesn’t check out with (z)grep 0 I’m using bcftools view -s to subset a VCF.gz file. I ran into an error: [E::vcf_parse_format] Number of columns at chr9:44897051 does not match the number of samples (90 vs 99) To look at this site, I ran…

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