Use 1000 Genomes reference assembly (http://www.1000genomes.org/category/reference; "phase2_reference_assembly_sequence" leads to "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/"; download "hs37d5.fa.gz" ) to circumvent the possible unmapped contigs as illustrated below.
##### ERROR MESSAGE: Input files /project/jferrer/EL/Gencode/gatk/dbsnp_138.b37.vcf and reference have incompatible contigs: No overlapping contigs found.
##### ERROR ~/EL/Gencode/gatk/dbsnp_138.b37.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT]
##### ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, GL877870.2, GL877872.1, GL383535.1, JH159133.1, KB663606.1, KB021647.1, KE332497.1, JH159131.1, GL949745.1, JH720447.1, GL582968.1, JH720446.1, JH591181.2, JH720443.2, JH159134.2, JH636052.4, JH636053.3, JH636054.1, JH636056.1, JH636058.1, JH636057.1, KE332505.1, JH720451.1, JH720452.1, JH720453.1, JH720454.3, JH159136.1, JH806587.1, JH806588.1, JH806589.1, JH806590.2, JH806591.1, JH806592.1, JH806593.1, JH806594.1, JH806595.1, JH806596.1, JH806597.1, JH720448.1, JH806598.1, JH806599.1, JH806600.2, JH806601.1, JH806602.1, JH806573.1, JH806574.2, JH806575.1, JH806580.1, JH806583.1, JH806584.1, JH806585.1, JH806603.1, JH159150.3, GL582969.1, JH806577.1, JH806578.1, JH806579.1, JH159137.1, KE332502.1, KB021645.1, KB663607.2, KE332500.1, KE332496.1, GL383558.1, GL582976.1, GL383523.1, KE332498.1, GL949743.1, KE332506.1, GL383536.1, JH591184.1, JH636061.1, JH806576.1, GL383524.1, GL582973.1, JH159138.1, KB021648.1, JH159139.1, JH159140.1, JH591182.1, JH159132.1, JH720449.1, JH591183.1, JH720444.2, JH159141.2, KB663604.1, JH720455.1, KB021646.2, JH159142.2, JH159143.1, JH806582.2, JH159135.2, KE332499.1, GL877877.2, JH806586.1, GL582979.2, KB663605.1, GL582975.1, GL949744.1, GL383543.1, GL877871.1, GL582967.1, JH159149.1, GL582977.2, GL582970.1, GL383559.2, JH159144.1, JH591186.1, GL383560.1, GL339450.1, GL582971.1, GL582974.1, JH806581.1, JH636060.1, JH591185.1, JH159145.1, GL877873.1, KB663608.1, GL582972.1, KB663603.1, KE332495.1, JH636059.1, JH720445.1, KE332501.1, GL383561.2, GL949741.1, GL383562.1, GL383525.1, GL383544.1, GL383548.1, GL383537.1, GL383538.1, GL383516.1, GL383517.1, GL383545.1, GL383546.1, GL383547.1, GL877875.1, GL383549.1, GL383550.1, GL383551.1, GL877876.1, GL383552.1, GL383553.2, GL383554.1, GL383555.1, GL383556.1, GL383557.1, GL000258.1, GL383563.2, GL383564.1, GL383565.1, GL383566.1, JH159146.1, JH159147.1, JH159148.1, GL383567.1, GL383568.1, GL383569.1, GL383570.1, GL383571.1, GL383572.1, GL949746.1, GL949747.1, GL949748.1, GL949749.1, GL949750.1, GL949751.1, GL949752.1, GL949753.1, GL383573.1, GL383574.1, GL383575.2, GL383576.1, GL383518.1, GL383519.1, GL383520.1, GL383577.1, GL383578.1, GL383579.1, GL383580.1, GL383581.1, GL383582.2, GL383583.1, KB663609.1, GL383521.1, GL383522.1, GL582966.2, JH636055.1, GL383526.1, GL000257.1, GL383527.1, GL383528.1, GL383529.1, GL339449.2, GL383530.1, GL383531.1, GL383532.1, GL949742.1, GL383533.1, KB021644.1, GL000250.1, GL000251.1, GL000252.1, GL000253.1, GL000254.1, GL000255.1, GL000256.1, GL383534.2, GL383539.1, GL383540.1, GL383541.1, GL383542.1, GL000191.1, GL000192.1, GL000193.1, GL000194.1, GL000195.1, GL000196.1, GL000197.1, GL000198.1, GL000199.1, GL000200.1, GL000201.1, GL000202.1, GL000203.1, GL000204.1, GL000205.1, GL000206.1, GL000207.1, GL000208.1, GL000209.1, GL000210.1, GL000211.1, GL000212.1, GL000213.1, GL000214.1, GL000215.1, GL000216.1, GL000217.1, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000222.1, GL000223.1, GL000224.1, GL000225.1, GL000226.1, GL000227.1, GL000228.1, GL000229.1, GL000230.1, GL000231.1, GL000232.1, GL000233.1, GL000234.1, GL000235.1, GL000236.1, GL000237.1, GL000238.1, GL000239.1, GL000240.1, GL000241.1, GL000242.1, GL000243.1, GL000244.1, GL000245.1, GL000246.1, GL000247.1, GL000248.1, GL000249.1]
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