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Output
Fritz Sedlazeck edited this page Jul 6, 2021
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Sniffles provide two different output formats VCF and BEDPE. Here we describe the different output and information that is provided.
The vcf format is a standard format for SNPs that got recently extended to structural variations. It follows a tab-delimited file with different information for each SVs:
| chromosome | The chromosome name where the SVs occurred |
| position | Starting breakpoint position of the SVs. |
| ID | the id of the SVs. SVs with the same ID belong together. They are indicated by _X, where X is an increasing number. |
| Ref | The sequence of the reference if not otherwise specified only an N. |
| Alt | Shows the type of the SVs. Sniffles report deletions (DEL), duplications (DUP), insertions (INS), inversion (INV) and translocations (TRA) as the standard types. Furthermore, we report inverted duplications (INVDUP). Sniffles report cases where it is not certain what type the SVs is e.g. DEL/INV. This field can also just be the sequence representing the insertion or deletion. |
| Quality | This is currently not indicated. |
| Filter | This is currently always set to be PASS or UNRESOLVED which means for insertions that the length could not have been resolved. |
| Info | Provides a list of information (see below) |
| FORMAT | Provides information about the next tag |
| Sample information | Depending on the way sniffles was run: Genotype estimation: Reads supporting the reference: Reads supporting the variant. |
Sniffles report multiple information in the Info field. The entries are delimited by ;.
| IMPRECISE/PRECISE | Indicates the confidence of the exact breakpoint positions (bp). |
| CHR2= | The chromosome of the second breakpoint of the SV reported. |
| END= | The position (bp) of the second breakpoint of the SV reported. |
| ZMW= | For PacBio based reads, shows the number of ZMW that support the SV. |
| SVTYPE= | The type of the SV. (see Alt field above) |
| SUPTYPE= | Indicates what evidence supports the SVs (SR: Split Reads, AL: Alignment, NR: Noisy Region). |
| STD_quant_start= | the standard deviation of the start breakpoints. |
| STD_quant_stop= | the standard deviation of the stop breakpoints. |
| RNAMES= | A comma-separated list of read names that support the SV event. Controlled by -n Parameter. |
| SVLEN= | Indicates the length of SVs. |
| STRANDS= | Strand information at both breakpoints. |
| RE= | Number of reads supporting the variance. |
| AF= | Allele frequency (only if run with –genotype) |
BEDPE format follows a bed file format, which is also tab-delimited.
| chromosome | The chromosome name where the SVs occurred |
| start | left most starting breakpoint position of the SVs |
| stop | right most starting breakpoint position of the SVs |
| chromosome | The chromosome name of the end breakpoint |
| start | left most end breakpoint position of the SVs |
| stop | right most end breakpoint position of the SVs |
| variant_name/ID | ID of the SVs |
| score | Score of the variant, currently not supported (-1). |
| strand1 | Strand information of the starting breakpoint. |
| strand2 | Strand information of the end breakpoint. |
| type | Type of the SVS (see above at VCF for further explanation) |
| number_of_reads | Number of reads supporting the SVs |
| best_chr1 | Chr of start position |
| best_start | Best estimation of Sniffles for the exact start position |
| best_chr2 | Chr of end position |
| best_stop | Best estimation of Sniffles for the exact stop position |
| predicted_length | Estimation of SVs length |