INV in ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz for NA20845 samtools view -b "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA20845/high_coverage_alignment/NA20845.wgs.ILLUMINA.bwa.GIH.high_cov_pcr_free.20140203.bam" "7:8352157-8356597"

7_8352157_8356597.svg

NA20845.txt

>>7/8353157/T (n. 1)
 Variant
 +-------+------------------------+
 | Key   | Value                  |
 +-------+------------------------+
 | CHROM | 7                      |
 | POS   | 8353157                |
 | end   | 8355597                |
 | ID    | CINV_delly_INV00091459 |
 | REF   | T                      |
 | ALT   | <INV>                  |
 | QUAL  |                        |
 | Type  | SYMBOLIC               |
 +-------+------------------------+
 Alleles
 +-----+-----+-----+-------+--------+-----+------+------+-----------------------+
 | Idx | REF | Sym | Bases | Length | HW  | AC   | AN   | AF                    |
 +-----+-----+-----+-------+--------+-----+------+------+-----------------------+
 | 0   | *   |     | T     | 1      |     | 4991 | 5008 | 0.9966054313099042    |
 | 1   |     | *   | <INV> |        | 1.0 | 17   | 5008 | 0.0033945686900958465 |
 +-----+-----+-----+-------+--------+-----+------+------+-----------------------+
 Hyperlinks
 +------------+-----------------------------------------------------------------------------------------------------------------------+
 | Name       | URL                                                                                                                   |
 +------------+-----------------------------------------------------------------------------------------------------------------------+
 | IGV        | https://127.0.0.1:60151/goto?locus=7%3A8353157-8355597                                                                |
 | UCSC hg19  | http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr7%3A8353157-8355597&position=chr7%3A8353107-8355647 |
 | clinvar 37 | https://www.ncbi.nlm.nih.gov/clinvar/?term=7%5Bchr%5D+AND+8353157%3A8355597%5Bchrpos37%5D                             |
 | decipher   | https://decipher.sanger.ac.uk/search?q=7%3A8353157-8355597                                                            |
 +------------+-----------------------------------------------------------------------------------------------------------------------+
 INFO
 +-----------+-------+------------+
 | key       | Index | Value      |
 +-----------+-------+------------+
 | AC        |       | 17         |
 | AF        |       | 0.00339457 |
 | AFR_AF    |       | 0          |
 | AMR_AF    |       | 0          |
 | AN        |       | 5008       |
 | CIEND     | 1     | -136       |
 | CIEND     | 2     | 136        |
 | CIPOS     | 1     | -136       |
 | CIPOS     | 2     | 136        |
 | CS        |       | CINV_delly |
 | EAS_AF    |       | 0          |
 | END       |       | 8355597    |
 | EUR_AF    |       | 0          |
 | IMPRECISE |       | true       |
 | NS        |       | 2504       |
 | SAS_AF    |       | 0.0174     |
 | SVTYPE    |       | INV        |
 +-----------+-------+------------+
 Genotype Types
 +---------+-------+----+
 | Type    | Count | %  |
 +---------+-------+----+
 | HOM_REF | 2487  | 99 |
 | HET     | 17    | 0  |
 +---------+-------+----+
 Genotypes
 +---------+------+-----+
 | Sample  | Type | GT  |
 +---------+------+-----+
 | HG02725 | HET  | 0|1 |
 | HG02734 | HET  | 1|0 |
 | HG03611 | HET  | 1|0 |
 | HG03681 | HET  | 0|1 |
 | HG03738 | HET  | 1|0 |
 | HG03789 | HET  | 0|1 |
 | HG03832 | HET  | 0|1 |
 | HG03869 | HET  | 1|0 |
 | HG03928 | HET  | 1|0 |
 | HG04093 | HET  | 1|0 |
 | HG04227 | HET  | 1|0 |
 | HG04235 | HET  | 0|1 |
 | NA20845 | HET  | 1|0 |
 | NA20869 | HET  | 0|1 |
 | NA20892 | HET  | 0|1 |
 | NA21125 | HET  | 0|1 |
 | NA21133 | HET  | 1|0 |
 +---------+------+-----+
<<7/8353157/T (n. 1)