![bam file format columns bam file format columns](https://image.slidesharecdn.com/cram-180923165549/95/cram-8-638.jpg)
Similarly, at least oneĪlternate allele from a multi-allelic VCF record must be present in the When multiple ALT alleles are present in the annotation file (given asĬomma-separated list of alleles), at least one must match one of theĪlleles in the corresponding VCF record. When REF and ALT are present, only matching VCF Note that in case of tab-delimited file, the coordinates POS, FROM and TO are The ".bed" or ".bed.gz" suffix (case-insensitive), otherwise a tab-delimited file is assumed. (or, alternatively, FROM and TO), optional columns REF and ALT, and arbitrary The fileĬan be VCF, BED, or a tab-delimited file with mandatory columns CHROM, POS Tags for the subset in another command one can pipe from view intoīgzip-compressed and tabix-indexed file with annotations. Option is used see bcftools view documentation). bcftools view is theĮxception where some tags will be updated (unless the -I, -no-update Note that in general tags such as INFO/AC, INFO/AN, etc are not updated The sample order is updated to reflect that given on the command line. s, -samples LISTĬomma-separated list of samples to include or exclude if prefixed This option requires indexed VCF/BCF files. Note that overlapping regions in FILE can result inĭuplicated out of order positions in the output. Processed in ascending genomic coordinate order no matter what order theyĪppear in FILE. However, within chromosomes, the VCF will always be The VCF will be processed in the order in which chromosomes first appear Also note that chromosome ordering in FILE will be respected, Note that sequence names must match exactly, "chr20" is not the same as Memory, while bgzip-compressed and tabix-indexed region files are streamed. Than the 1-based tab-delimited file, the file must have the ".bed" or To indicate that a file be treated as BED rather The columns of the tab-delimited BED file are alsoĬHROM, POS and END (trailing columns are ignored), but coordinatesĪre 0-based, half-open. The columns of the tab-delimited fileĬan contain either positions (two-column format) or intervals (three-columnįormat): CHROM, POS, and, optionally, END, where positions are 1-basedĪnd inclusive. Regions can be specified either on command line or in a VCF, BED, or
![bam file format columns bam file format columns](https://www.genomatix.de/online_help/help_regionminer/bam_tools_overview.png)
Note that -r cannot be used in combination with -R. Region, unlike the -t/-T options where only the POS coordinate is checked. Records are matched even when the starting coordinate is outside of the r, -regions chr| chr:pos| chr:beg-end| chr:beg-Ĭomma-separated list of regions, see also -R, -regions-file. Performance by removing unnecessary compression/decompression and Use the -Ou option when piping between bcftools subcommands to speed up Output compressed BCF ( b), uncompressed BCF ( u), compressed VCF ( z), uncompressed VCF ( v). To standard output, where it is written by default. When output consists of a single stream, write it to FILE rather than For example, to include only sites which have no filters set,ĭo not append version and command line information to the output VCF header. Skip sites where FILTER column does not contain any of the strings listed Only records with identical ID column are compatible. For duplicate positions, only theįirst indel record will be considered and appear on output. indelsĪll indel records are compatible, regardless of whether the REFĪnd ALT alleles match or not. Record will be considered and appear on output.
![bam file format columns bam file format columns](https://i.ytimg.com/vi/5VEjmXt6sqU/mqdefault.jpg)
For duplicate positions, only the first SNP snpsĪny SNP records are compatible, regardless of whether the ALTĪlleles match or not. The first will be considered and appear on output.
![bam file format columns bam file format columns](https://crossmap.readthedocs.io/en/latest/_images/howitworks.png)
In the case of records with the same position, only Only records where some subset of ALT alleles match are compatible allĪll records are compatible, regardless of whether the ALT alleles Only records with identical REF and ALT alleles are compatible some